diff --git a/packages/kbn-docs-utils/src/build_api_docs_cli.test.ts b/packages/kbn-docs-utils/src/build_api_docs_cli.test.ts
index 7dd4f139ac9a3..7b2b92c66d047 100644
--- a/packages/kbn-docs-utils/src/build_api_docs_cli.test.ts
+++ b/packages/kbn-docs-utils/src/build_api_docs_cli.test.ts
@@ -82,11 +82,13 @@ describe('build_api_docs_cli', () => {
   });
 
   it('runs build flow when stats are not provided', async () => {
+    const mockPlugins = [
+      { id: 'p1', manifest: { owner: { name: 'team' }, serviceFolders: [] }, isPlugin: true },
+    ];
     const setupResult = {
       project: {},
-      plugins: [
-        { id: 'p1', manifest: { owner: { name: 'team' }, serviceFolders: [] }, isPlugin: true },
-      ],
+      plugins: mockPlugins,
+      allPlugins: mockPlugins,
     };
     const apiMapResult = {
       pluginApiMap: {},
@@ -107,6 +109,7 @@ describe('build_api_docs_cli', () => {
     expect(buildApiMap).toHaveBeenCalledWith(
       setupResult.project,
       setupResult.plugins,
+      setupResult.allPlugins,
       log,
       mockTx,
       { stats: undefined, collectReferences: false }
diff --git a/packages/kbn-docs-utils/src/build_api_docs_cli.ts b/packages/kbn-docs-utils/src/build_api_docs_cli.ts
index 5f3a42709ba45..25ab26c60f740 100644
--- a/packages/kbn-docs-utils/src/build_api_docs_cli.ts
+++ b/packages/kbn-docs-utils/src/build_api_docs_cli.ts
@@ -85,6 +85,7 @@ export function runBuildApiDocsCli() {
       const apiMapResult = buildApiMap(
         setupResult.project,
         setupResult.plugins,
+        setupResult.allPlugins,
         log,
         transaction,
         options
diff --git a/packages/kbn-docs-utils/src/check_package_docs_cli.run.test.ts b/packages/kbn-docs-utils/src/check_package_docs_cli.run.test.ts
index 893bad4980a78..b884fc0ccd31c 100644
--- a/packages/kbn-docs-utils/src/check_package_docs_cli.run.test.ts
+++ b/packages/kbn-docs-utils/src/check_package_docs_cli.run.test.ts
@@ -90,7 +90,7 @@ describe('runCheckPackageDocs', () => {
     expect(reportMetrics).toHaveBeenCalled();
     expect(process.exitCode).toBe(1);
     expect(log.error).toHaveBeenCalledWith(
-      expect.stringContaining('Validation failed for 1 plugin')
+      expect.stringContaining('Validation failed for 1 package')
     );
     expect(mockTx.end).toHaveBeenCalled();
   });
@@ -129,7 +129,7 @@ describe('runCheckPackageDocs', () => {
     await runCheckPackageDocs(log as any, { plugin: 'plugin-a' } as any);
 
     expect(process.exitCode).toBeUndefined();
-    expect(log.info).toHaveBeenCalledWith('All plugins passed validation.');
+    expect(log.info).toHaveBeenCalledWith('All packages passed validation.');
     expect(mockTx.end).toHaveBeenCalled();
   });
 });
diff --git a/packages/kbn-docs-utils/src/check_package_docs_cli.ts b/packages/kbn-docs-utils/src/check_package_docs_cli.ts
index 055a6bccb4521..489703bf4e8ba 100644
--- a/packages/kbn-docs-utils/src/check_package_docs_cli.ts
+++ b/packages/kbn-docs-utils/src/check_package_docs_cli.ts
@@ -129,6 +129,7 @@ export const runCheckPackageDocs = async (log: ToolingLog, flags: CliFlags) => {
     const apiMapResult = buildApiMap(
       setupResult.project,
       setupResult.plugins,
+      setupResult.allPlugins,
       log,
       transaction,
       optionsWithChecks
@@ -160,13 +161,13 @@ export const runCheckPackageDocs = async (log: ToolingLog, flags: CliFlags) => {
 
     if (failingPlugins.length > 0) {
       log.error(
-        `Validation failed for ${failingPlugins.length} plugin(s): ${failingPlugins
-          .map((plugin) => plugin.pluginId)
+        `Validation failed for ${failingPlugins.length} package(s): ${failingPlugins
+          .map(({ pluginId }) => pluginId)
           .join(', ')}.`
       );
       process.exitCode = 1;
     } else {
-      log.info('All plugins passed validation.');
+      log.info('All packages passed validation.');
     }
   } catch (error) {
     transaction?.setOutcome('failure');
diff --git a/packages/kbn-docs-utils/src/cli/tasks/build_api_map.test.ts b/packages/kbn-docs-utils/src/cli/tasks/build_api_map.test.ts
index 495960ad9e59f..3c2da2fdfe245 100644
--- a/packages/kbn-docs-utils/src/cli/tasks/build_api_map.test.ts
+++ b/packages/kbn-docs-utils/src/cli/tasks/build_api_map.test.ts
@@ -67,9 +67,10 @@ describe('buildApiMap', () => {
       pluginFilter: ['test-plugin'],
     };
 
-    buildApiMap(project, plugins, log, transaction, options);
+    const allPlugins = [...plugins, { id: 'other-plugin' }];
+    buildApiMap(project, plugins, allPlugins, log, transaction, options);
 
-    expect(getPluginApiMap).toHaveBeenCalledWith(project, plugins, log, {
+    expect(getPluginApiMap).toHaveBeenCalledWith(project, plugins, allPlugins, log, {
       collectReferences: true,
       pluginFilter: ['test-plugin'],
     });
@@ -80,7 +81,7 @@ describe('buildApiMap', () => {
       collectReferences: false,
     };
 
-    const result = buildApiMap(project, plugins, log, transaction, options);
+    const result = buildApiMap(project, plugins, plugins, log, transaction, options);
 
     expect(result).toBeDefined();
     expect(result.pluginApiMap).toBeDefined();
@@ -95,7 +96,7 @@ describe('buildApiMap', () => {
       collectReferences: false,
     };
 
-    buildApiMap(project, plugins, log, transaction, options);
+    buildApiMap(project, plugins, plugins, log, transaction, options);
 
     expect(transaction.startSpan).toHaveBeenCalledWith('build_api_docs.getPluginApiMap', 'setup');
   });
diff --git a/packages/kbn-docs-utils/src/cli/tasks/build_api_map.ts b/packages/kbn-docs-utils/src/cli/tasks/build_api_map.ts
index 50ea9ffc55f7a..d8b60f5ea9574 100644
--- a/packages/kbn-docs-utils/src/cli/tasks/build_api_map.ts
+++ b/packages/kbn-docs-utils/src/cli/tasks/build_api_map.ts
@@ -25,6 +25,7 @@ import type { BuildApiMapResult, CliOptions } from '../types';
  *
  * @param project - TypeScript project instance.
  * @param plugins - List of plugins and packages to analyze.
+ * @param allPlugins - All plugins/packages for cross-reference resolution.
  * @param log - Tooling log instance.
  * @param transaction - APM transaction for tracking.
  * @param options - CLI options including collectReferences and pluginFilter.
@@ -33,6 +34,7 @@ import type { BuildApiMapResult, CliOptions } from '../types';
 export function buildApiMap(
   project: Project,
   plugins: PluginOrPackage[],
+  allPlugins: PluginOrPackage[],
   log: ToolingLog,
   transaction: Transaction,
   options: CliOptions
@@ -46,7 +48,7 @@ export function buildApiMap(
     referencedDeprecations,
     adoptionTrackedAPIs,
     unnamedExports,
-  } = getPluginApiMap(project, plugins, log, {
+  } = getPluginApiMap(project, plugins, allPlugins, log, {
     collectReferences: options.collectReferences,
     pluginFilter: options.pluginFilter,
   });
diff --git a/packages/kbn-docs-utils/src/cli/tasks/collect_stats.test.ts b/packages/kbn-docs-utils/src/cli/tasks/collect_stats.test.ts
index 72f8095161742..279aca334bd12 100644
--- a/packages/kbn-docs-utils/src/cli/tasks/collect_stats.test.ts
+++ b/packages/kbn-docs-utils/src/cli/tasks/collect_stats.test.ts
@@ -55,6 +55,7 @@ describe('collectStats', () => {
       plugins: [mockPlugin],
       pathsByPlugin: new Map([[mockPlugin, ['src/plugins/test/public/index.ts']]]),
       project: {} as any,
+      allPlugins: [mockPlugin],
     };
 
     apiMapResult = {
diff --git a/packages/kbn-docs-utils/src/cli/tasks/report_metrics.test.ts b/packages/kbn-docs-utils/src/cli/tasks/report_metrics.test.ts
index 9baf46192ecf5..56a6a48812675 100644
--- a/packages/kbn-docs-utils/src/cli/tasks/report_metrics.test.ts
+++ b/packages/kbn-docs-utils/src/cli/tasks/report_metrics.test.ts
@@ -64,6 +64,7 @@ describe('reportMetrics', () => {
       plugins: [mockPlugin],
       pathsByPlugin: new Map(),
       project: {} as any,
+      allPlugins: [mockPlugin],
     };
 
     apiMapResult = {
diff --git a/packages/kbn-docs-utils/src/cli/tasks/report_metrics.ts b/packages/kbn-docs-utils/src/cli/tasks/report_metrics.ts
index fc3d467712439..1bb3da436de88 100644
--- a/packages/kbn-docs-utils/src/cli/tasks/report_metrics.ts
+++ b/packages/kbn-docs-utils/src/cli/tasks/report_metrics.ts
@@ -16,10 +16,17 @@ import type { AllPluginStats, BuildApiMapResult, CliOptions, SetupProjectResult
 /**
  * Generates a link to the GitHub source for an API declaration.
  *
+ * TODO: clintandrewhall - allow `base` to be overridden in the instance of a CI build
+ * associated with a PR.
+ *
  * @param declaration - API declaration to generate link for.
  * @returns GitHub link to the source code.
  */
 function getLink(declaration: ApiDeclaration): string {
+  const base = `https://github.com/elastic/kibana/blob/main/${declaration.path}`;
+  if (declaration.lineNumber) {
+    return `${base}#L${declaration.lineNumber}`;
+  }
   return `https://github.com/elastic/kibana/tree/main/${
     declaration.path
   }#:~:text=${encodeURIComponent(declaration.label)}`;
@@ -53,10 +60,38 @@ export function reportMetrics(
   const { missingApiItems, referencedDeprecations } = apiMapResult;
   const reporter = CiStatsReporter.fromEnv(log);
 
+  const printIssueTable = (title: string, rows: Array<{ id: string; link: string }>) => {
+    const count = rows.length;
+    if (count === 0) {
+      log.info(`${title}: none`);
+      return;
+    }
+    log.info(`${title} (${count})`);
+    // eslint-disable-next-line no-console
+    console.table(rows);
+  };
+
+  const printMissingExportsTable = (
+    title: string,
+    entries: Array<{ source: string; references: string }>
+  ) => {
+    const header = title.toUpperCase();
+    const count = entries.length;
+    if (count === 0) {
+      log.info(`${header}: none`);
+      return;
+    }
+    log.info(`${header} (${count})`);
+    // eslint-disable-next-line no-console
+    console.table(
+      entries.map(({ source, references }) => ({
+        'Not exported source': source,
+        references,
+      }))
+    );
+  };
+
   for (const plugin of plugins) {
-    // Note that the filtering is done here (per-plugin), rather than earlier in the pipeline.
-    // This keeps the metrics task aligned with how other docs tasks process plugins and ensures
-    // that all plugin data has been collected before selectively reporting metrics.
     if (options.pluginFilter && !options.pluginFilter.includes(plugin.id)) {
       continue;
     }
@@ -162,7 +197,7 @@ export function reportMetrics(
         // eslint-disable-next-line no-console
         console.table(referencedDeprecations[id]);
       } else {
-        log.info(`No referenced deprecations for plugin ${plugin.id}`);
+        log.info(`No referenced deprecations for ${plugin.id}`);
       }
       if (pluginStats.noReferences.length > 0) {
         // eslint-disable-next-line no-console
@@ -173,7 +208,7 @@ export function reportMetrics(
           }))
         );
       } else {
-        log.info(`No unused APIs for plugin ${plugin.id}`);
+        log.info(`No unused APIs for ${plugin.id}`);
       }
     }
 
@@ -184,14 +219,12 @@ export function reportMetrics(
         pluginStats.deprecatedAPIsReferencedCount === 0 &&
         (!missingApiItems[id] || Object.keys(missingApiItems[id]).length === 0);
 
-      log.info(`--- Plugin '${id}' ${passesAllChecks ? 'passes all checks ----' : '----'}`);
+      log.info(`--- '${id}' ${passesAllChecks ? 'passes all checks ----' : '----'}`);
 
       if (!passesAllChecks) {
-        log.info(`${pluginStats.isAnyType.length} API items with ANY`);
-
         if (options.stats.includes('any')) {
-          // eslint-disable-next-line no-console
-          console.table(
+          printIssueTable(
+            'API items with ANY',
             pluginStats.isAnyType.map((d) => ({
               id: d.id,
               link: getLink(d),
@@ -199,10 +232,9 @@ export function reportMetrics(
           );
         }
 
-        log.info(`${pluginStats.missingComments.length} API items missing comments`);
         if (options.stats.includes('comments')) {
-          // eslint-disable-next-line no-console
-          console.table(
+          printIssueTable(
+            'API items missing comments',
             pluginStats.missingComments.map((d) => ({
               id: d.id,
               link: getLink(d),
@@ -211,15 +243,12 @@ export function reportMetrics(
         }
 
         if (missingApiItems[id]) {
-          log.info(`${Object.keys(missingApiItems[id]).length} referenced API items not exported`);
           if (options.stats.includes('exports')) {
-            // eslint-disable-next-line no-console
-            console.table(
-              Object.keys(missingApiItems[id]).map((key) => ({
-                'Not exported source': key,
-                references: missingApiItems[id][key].join(', '),
-              }))
-            );
+            const exportsTable = Object.keys(missingApiItems[id]).map((key) => ({
+              source: key,
+              references: missingApiItems[id][key].join(', '),
+            }));
+            printMissingExportsTable('Referenced API items not exported', exportsTable);
           }
         }
       }
diff --git a/packages/kbn-docs-utils/src/cli/tasks/setup_project.test.ts b/packages/kbn-docs-utils/src/cli/tasks/setup_project.test.ts
index 4009496c575b9..42a555809fe2e 100644
--- a/packages/kbn-docs-utils/src/cli/tasks/setup_project.test.ts
+++ b/packages/kbn-docs-utils/src/cli/tasks/setup_project.test.ts
@@ -11,6 +11,7 @@ import Path from 'path';
 import { ToolingLog } from '@kbn/tooling-log';
 import { setupProject } from './setup_project';
 import type { CliContext, CliOptions } from '../types';
+import type { FindPluginsOptions } from '../../find_plugins';
 
 // Mock dependencies - order matters: mock get_all_doc_file_ids first to prevent globby from loading
 jest.mock('../../mdx/get_all_doc_file_ids', () => ({
@@ -112,6 +113,7 @@ describe('setupProject', () => {
     const result = await setupProject(context, options);
 
     expect(result.plugins).toBeDefined();
+    expect(result.allPlugins).toBeDefined();
     expect(result.pathsByPlugin).toBeDefined();
     expect(result.project).toBeDefined();
   });
@@ -134,9 +136,21 @@ describe('setupProject', () => {
     const Fs = jest.requireMock('fs');
     Fs.existsSync.mockReturnValue(true);
 
-    (findPlugins as jest.Mock).mockReturnValue([
-      { id: 'test-plugin', isPlugin: true, directory: '/tmp/test' },
-    ]);
+    const mockPlugin = {
+      id: 'test-plugin',
+      directory: '/mock/repo/root/src/plugins/test',
+      isPlugin: true,
+      manifest: { id: 'test-plugin', owner: { name: 'test-team' }, serviceFolders: [] },
+      manifestPath: '/mock/repo/root/src/plugins/test/kibana.json',
+    };
+
+    // Return all plugins for allPlugins, filtered for filteredPlugins
+    (findPlugins as jest.Mock).mockImplementation((options?: FindPluginsOptions) => {
+      if (options?.pluginFilter) {
+        return [mockPlugin];
+      }
+      return [mockPlugin, { ...mockPlugin, id: 'other-plugin' }];
+    });
 
     const options: CliOptions = {
       collectReferences: false,
@@ -173,4 +187,76 @@ describe('setupProject', () => {
       "expected --package '@kbn/nonexistent-package' was not found"
     );
   });
+
+  it('scopes TypeScript project to single plugin directory when pluginFilter has one plugin', async () => {
+    const { Project } = jest.requireMock('ts-morph');
+    const mockProject = Project();
+
+    jest.clearAllMocks();
+
+    const mockPlugin = {
+      id: 'single-plugin',
+      directory: '/mock/repo/root/src/plugins/single',
+      isPlugin: true,
+      manifest: { id: 'single-plugin', owner: { name: 'test-team' }, serviceFolders: [] },
+      manifestPath: '/mock/repo/root/src/plugins/single/kibana.json',
+    };
+
+    // Return all plugins for allPlugins, filtered for plugins
+    (findPlugins as jest.Mock).mockImplementation((options?: FindPluginsOptions) => {
+      if (options?.pluginFilter) {
+        return [mockPlugin];
+      }
+      return [mockPlugin, { ...mockPlugin, id: 'other-plugin' }];
+    });
+
+    const options: CliOptions = {
+      collectReferences: false,
+      pluginFilter: ['single-plugin'],
+    };
+
+    await setupProject(context, options);
+
+    // Should use the single plugin's tsconfig
+    expect(Project).toHaveBeenCalledWith({
+      tsConfigFilePath: '/mock/repo/root/src/plugins/single/tsconfig.json',
+      skipAddingFilesFromTsConfig: true,
+    });
+
+    // Should only add files from the single plugin directory
+    expect(mockProject.addSourceFilesAtPaths).toHaveBeenCalledWith([
+      '/mock/repo/root/src/plugins/single/**/*.ts',
+      '!**/*.d.ts',
+    ]);
+
+    // Should NOT call resolveSourceFileDependencies for single-plugin builds
+    expect(mockProject.resolveSourceFileDependencies).not.toHaveBeenCalled();
+  });
+
+  it('loads full codebase and resolves dependencies when no pluginFilter', async () => {
+    const { Project } = jest.requireMock('ts-morph');
+    const mockProject = Project();
+
+    jest.clearAllMocks();
+
+    (findPlugins as jest.Mock).mockReturnValue([]);
+
+    const options: CliOptions = {
+      collectReferences: false,
+    };
+
+    await setupProject(context, options);
+
+    // Should use the repo root tsconfig
+    expect(Project).toHaveBeenCalledWith({
+      tsConfigFilePath: '/mock/repo/root/tsconfig.json',
+      skipAddingFilesFromTsConfig: true,
+    });
+
+    // Should add files from all directories
+    expect(mockProject.addSourceFilesAtPaths).toHaveBeenCalledTimes(8);
+
+    // Should call resolveSourceFileDependencies for full builds
+    expect(mockProject.resolveSourceFileDependencies).toHaveBeenCalled();
+  });
 });
diff --git a/packages/kbn-docs-utils/src/cli/tasks/setup_project.ts b/packages/kbn-docs-utils/src/cli/tasks/setup_project.ts
index f8c828945a037..5c5368dc5e3bf 100644
--- a/packages/kbn-docs-utils/src/cli/tasks/setup_project.ts
+++ b/packages/kbn-docs-utils/src/cli/tasks/setup_project.ts
@@ -36,6 +36,7 @@ function getTsProject(repoPath: string, overridePath?: string): Project {
   });
 
   if (!overridePath) {
+    // Full build: load all source files and resolve dependencies upfront
     project.addSourceFilesAtPaths([`${repoPath}/x-pack/plugins/**/*.ts`, '!**/*.d.ts']);
     project.addSourceFilesAtPaths([`${repoPath}/x-pack/packages/**/*.ts`, '!**/*.d.ts']);
     project.addSourceFilesAtPaths([`${repoPath}/x-pack/platform/**/*.ts`, '!**/*.d.ts']);
@@ -44,10 +45,17 @@ function getTsProject(repoPath: string, overridePath?: string): Project {
     project.addSourceFilesAtPaths([`${repoPath}/src/platform/**/*.ts`, '!**/*.d.ts']);
     project.addSourceFilesAtPaths([`${repoPath}/src/core/packages/**/*.ts`, '!**/*.d.ts']);
     project.addSourceFilesAtPaths([`${repoPath}/packages/**/*.ts`, '!**/*.d.ts']);
+    project.resolveSourceFileDependencies();
   } else {
+    // Single-plugin build: only load files from the target plugin directory.
+    // We intentionally skip resolveSourceFileDependencies() here because:
+    // 1. ts-morph resolves dependencies lazily when accessed (e.g., via getType()).
+    // 2. This significantly reduces memory usage and startup time for single-plugin builds.
+    // 3. Cross-package type references still resolve correctly via the tsconfig paths.
+    // Trade-off: First access to external types may be slightly slower, but overall
+    // build time is reduced since we don't load the entire codebase into memory.
     project.addSourceFilesAtPaths([`${overridePath}/**/*.ts`, '!**/*.d.ts']);
   }
-  project.resolveSourceFileDependencies();
   return project;
 }
 
@@ -84,11 +92,14 @@ export async function setupProject(
   spanInitialDocIds?.end();
 
   const spanPlugins = transaction.startSpan('build_api_docs.findPlugins', 'setup');
-  const plugins = hasAnyFilter ? findPlugins({ pluginFilter, packageFilter }) : findPlugins();
+  // Always find all plugins for cross-reference resolution.
+  const allPlugins = findPlugins();
+  // Find filtered plugins if a filter is provided.
+  const filteredPlugins = hasAnyFilter ? findPlugins({ pluginFilter, packageFilter }) : allPlugins;
 
   // Validate that all requested plugins were found.
   if (hasPluginFilter && pluginFilter) {
-    const foundPluginIds = plugins.filter((p) => p.isPlugin).map((p) => p.id);
+    const foundPluginIds = filteredPlugins.filter((p) => p.isPlugin).map((p) => p.id);
     const missingPlugins = pluginFilter.filter((id) => !foundPluginIds.includes(id));
     if (missingPlugins.length > 0) {
       throw createFlagError(`expected --plugin '${missingPlugins.join(', ')}' was not found`);
@@ -97,12 +108,15 @@ export async function setupProject(
 
   // Validate that all requested packages were found.
   if (hasPackageFilter && packageFilter) {
-    const foundPackageIds = plugins.filter((p) => !p.isPlugin).map((p) => p.id);
+    const foundPackageIds = filteredPlugins.filter((p) => !p.isPlugin).map((p) => p.id);
     const missingPackages = packageFilter.filter((id) => !foundPackageIds.includes(id));
     if (missingPackages.length > 0) {
       throw createFlagError(`expected --package '${missingPackages.join(', ')}' was not found`);
     }
   }
+
+  // Use filtered plugins for iteration, all plugins for reference resolution
+  const plugins = hasAnyFilter ? filteredPlugins : allPlugins;
   spanPlugins?.end();
 
   const spanPathsByPackage = transaction.startSpan('build_api_docs.getPathsByPackage', 'setup');
@@ -112,7 +126,7 @@ export async function setupProject(
   const spanProject = transaction.startSpan('build_api_docs.getTsProject', 'setup');
   // Optimize: when building a single plugin/package, scope the TS project to just that directory
   const singlePluginDirectory =
-    hasAnyFilter && plugins.length === 1 ? plugins[0].directory : undefined;
+    hasAnyFilter && filteredPlugins.length === 1 ? filteredPlugins[0].directory : undefined;
   const project = getTsProject(REPO_ROOT, singlePluginDirectory);
   spanProject?.end();
 
@@ -130,6 +144,7 @@ export async function setupProject(
 
   return {
     plugins,
+    allPlugins,
     pathsByPlugin,
     project,
     initialDocIds,
diff --git a/packages/kbn-docs-utils/src/cli/tasks/write_docs.test.ts b/packages/kbn-docs-utils/src/cli/tasks/write_docs.test.ts
index 67ada62f759ef..e11defe651cb6 100644
--- a/packages/kbn-docs-utils/src/cli/tasks/write_docs.test.ts
+++ b/packages/kbn-docs-utils/src/cli/tasks/write_docs.test.ts
@@ -69,6 +69,7 @@ describe('writeDocs', () => {
       pathsByPlugin: new Map(),
       project: {} as any,
       initialDocIds: ['doc1', 'doc2'],
+      allPlugins: [mockPlugin],
     };
 
     apiMapResult = {
@@ -155,6 +156,34 @@ describe('writeDocs', () => {
     expect(writePluginDocs).toHaveBeenCalled();
   });
 
+  it('skips aggregate docs when pluginFilter is provided', async () => {
+    const options: CliOptions = {
+      collectReferences: false,
+      pluginFilter: ['test-plugin'],
+    };
+
+    await writeDocs(context, setupResult, apiMapResult, allPluginStats, options);
+
+    expect(writePluginDirectoryDoc).not.toHaveBeenCalled();
+    expect(writeDeprecationDocByPlugin).not.toHaveBeenCalled();
+    expect(writeDeprecationDueByTeam).not.toHaveBeenCalled();
+    expect(writeDeprecationDocByApi).not.toHaveBeenCalled();
+  });
+
+  it('skips aggregate docs when packageFilter is provided', async () => {
+    const options: CliOptions = {
+      collectReferences: false,
+      packageFilter: ['@kbn/test-package'],
+    };
+
+    await writeDocs(context, setupResult, apiMapResult, allPluginStats, options);
+
+    expect(writePluginDirectoryDoc).not.toHaveBeenCalled();
+    expect(writeDeprecationDocByPlugin).not.toHaveBeenCalled();
+    expect(writeDeprecationDueByTeam).not.toHaveBeenCalled();
+    expect(writeDeprecationDocByApi).not.toHaveBeenCalled();
+  });
+
   it('trims deleted docs from nav when initialDocIds are provided', async () => {
     const options: CliOptions = {
       collectReferences: false,
diff --git a/packages/kbn-docs-utils/src/cli/tasks/write_docs.ts b/packages/kbn-docs-utils/src/cli/tasks/write_docs.ts
index 0a6e6388d7c7d..343092f5f7d85 100644
--- a/packages/kbn-docs-utils/src/cli/tasks/write_docs.ts
+++ b/packages/kbn-docs-utils/src/cli/tasks/write_docs.ts
@@ -45,24 +45,51 @@ export async function writeDocs(
 ): Promise<void> {
   const { log, transaction, outputFolder } = context;
   const { initialDocIds } = setupResult;
-  const { plugins } = setupResult;
+  const { plugins, allPlugins } = setupResult;
   const { pluginApiMap, referencedDeprecations, unreferencedDeprecations } = apiMapResult;
 
-  if (!options.stats) {
+  // Only write aggregate docs (plugin directory, deprecation summaries) for full builds.
+  // Filtered builds skip these because:
+  // 1. Aggregate docs require complete data from all plugins to be accurate.
+  // 2. Writing partial deprecation data would be misleading (e.g., "deprecation by team").
+  // 3. Single-plugin builds focus on validating that plugin's docs only.
+  const hasFilter = options.pluginFilter?.length || options.packageFilter?.length;
+  if (!options.stats && !hasFilter) {
     const spanWritePluginDirectoryDoc = transaction.startSpan(
       'build_api_docs.writePluginDirectoryDoc',
       'write'
     );
-
     await writePluginDirectoryDoc(outputFolder, pluginApiMap, allPluginStats, log);
-
     spanWritePluginDirectoryDoc?.end();
+
+    const spanWriteDeprecationDocByPlugin = transaction.startSpan(
+      'build_api_docs.writeDeprecationDocByPlugin',
+      'write'
+    );
+    await writeDeprecationDocByPlugin(outputFolder, referencedDeprecations, log);
+    spanWriteDeprecationDocByPlugin?.end();
+
+    const spanWriteDeprecationDueByTeam = transaction.startSpan(
+      'build_api_docs.writeDeprecationDueByTeam',
+      'write'
+    );
+    await writeDeprecationDueByTeam(outputFolder, referencedDeprecations, allPlugins, log);
+    spanWriteDeprecationDueByTeam?.end();
+
+    const spanWriteDeprecationDocByApi = transaction.startSpan(
+      'build_api_docs.writeDeprecationDocByApi',
+      'write'
+    );
+    await writeDeprecationDocByApi(
+      outputFolder,
+      referencedDeprecations,
+      unreferencedDeprecations,
+      log
+    );
+    spanWriteDeprecationDocByApi?.end();
   }
 
   for (const plugin of plugins) {
-    // Note that the filtering is done in this task, and not during plugin discovery, because the entire
-    // public plugin API has to be parsed in order to correctly determine reference links, and ensure that
-    // `removeBrokenLinks` doesn't remove more links than necessary.
     if (options.pluginFilter && !options.pluginFilter.includes(plugin.id)) {
       continue;
     }
@@ -73,7 +100,7 @@ export async function writeDocs(
 
     if (!options.stats) {
       if (pluginStats.apiCount > 0) {
-        log.info(`Writing public API doc for plugin ${pluginApi.id}.`);
+        log.info(`Writing public API doc for ${pluginApi.id}.`);
 
         const spanWritePluginDocs = transaction.startSpan(
           'build_api_docs.writePluginDocs',
@@ -84,40 +111,8 @@ export async function writeDocs(
 
         spanWritePluginDocs?.end();
       } else {
-        log.info(`Plugin ${pluginApi.id} has no public API.`);
+        log.info(`${pluginApi.id} has no public API.`);
       }
-
-      const spanWriteDeprecationDocByPlugin = transaction.startSpan(
-        'build_api_docs.writeDeprecationDocByPlugin',
-        'write'
-      );
-
-      await writeDeprecationDocByPlugin(outputFolder, referencedDeprecations, log);
-
-      spanWriteDeprecationDocByPlugin?.end();
-
-      const spanWriteDeprecationDueByTeam = transaction.startSpan(
-        'build_api_docs.writeDeprecationDueByTeam',
-        'write'
-      );
-
-      await writeDeprecationDueByTeam(outputFolder, referencedDeprecations, plugins, log);
-
-      spanWriteDeprecationDueByTeam?.end();
-
-      const spanWriteDeprecationDocByApi = transaction.startSpan(
-        'build_api_docs.writeDeprecationDocByApi',
-        'write'
-      );
-
-      await writeDeprecationDocByApi(
-        outputFolder,
-        referencedDeprecations,
-        unreferencedDeprecations,
-        log
-      );
-
-      spanWriteDeprecationDocByApi?.end();
     }
   }
 
diff --git a/packages/kbn-docs-utils/src/cli/types.ts b/packages/kbn-docs-utils/src/cli/types.ts
index b2e3fa26b8ae4..ea6bfb18cd878 100644
--- a/packages/kbn-docs-utils/src/cli/types.ts
+++ b/packages/kbn-docs-utils/src/cli/types.ts
@@ -72,8 +72,10 @@ export interface CliContext {
  * Result from setup_project task.
  */
 export interface SetupProjectResult {
-  /** Discovered plugins and packages. */
+  /** Plugins/packages to analyze (may be filtered via --plugin/--package). */
   plugins: PluginOrPackage[];
+  /** All discovered plugins/packages (for cross-reference resolution). */
+  allPlugins: PluginOrPackage[];
   /** File paths grouped by package. */
   pathsByPlugin: Map<PluginOrPackage, string[]>;
   /** TypeScript project instance. */
diff --git a/packages/kbn-docs-utils/src/count_eslint_disable.test.ts b/packages/kbn-docs-utils/src/count_eslint_disable.test.ts
index 6bd081a13f049..1a31c1f3eb288 100644
--- a/packages/kbn-docs-utils/src/count_eslint_disable.test.ts
+++ b/packages/kbn-docs-utils/src/count_eslint_disable.test.ts
@@ -34,7 +34,7 @@ describe('countEslintDisableLines', () => {
     expect(counts).toMatchInlineSnapshot(`
       Object {
         "eslintDisableFileCount": 3,
-        "eslintDisableLineCount": 9,
+        "eslintDisableLineCount": 8,
       }
     `);
   });
diff --git a/packages/kbn-docs-utils/src/get_plugin_api_map.test.ts b/packages/kbn-docs-utils/src/get_plugin_api_map.test.ts
index c2e037944ddf1..f22f83522a0df 100644
--- a/packages/kbn-docs-utils/src/get_plugin_api_map.test.ts
+++ b/packages/kbn-docs-utils/src/get_plugin_api_map.test.ts
@@ -39,7 +39,7 @@ describe('getPluginApiMap', () => {
     );
     const plugins = [pluginA, pluginB];
 
-    const result = getPluginApiMap(project, plugins, log, {
+    const result = getPluginApiMap(project, plugins, plugins, log, {
       collectReferences: false,
     });
 
@@ -54,7 +54,7 @@ describe('getPluginApiMap', () => {
     const pluginA = getKibanaPlatformPlugin('pluginA');
     const plugins = [pluginA];
 
-    const result = getPluginApiMap(project, plugins, log, {
+    const result = getPluginApiMap(project, plugins, plugins, log, {
       collectReferences: false,
     });
 
@@ -67,7 +67,7 @@ describe('getPluginApiMap', () => {
     const pluginA = getKibanaPlatformPlugin('pluginA');
     const plugins = [pluginA];
 
-    const result = getPluginApiMap(project, plugins, log, {
+    const result = getPluginApiMap(project, plugins, plugins, log, {
       collectReferences: true,
     });
 
@@ -79,7 +79,7 @@ describe('getPluginApiMap', () => {
     const pluginA = getKibanaPlatformPlugin('pluginA');
     const plugins = [pluginA];
 
-    const result = getPluginApiMap(project, plugins, log, {
+    const result = getPluginApiMap(project, plugins, plugins, log, {
       collectReferences: false,
     });
 
@@ -96,7 +96,7 @@ describe('getPluginApiMap', () => {
     );
     const plugins = [pluginA, pluginB];
 
-    const result = getPluginApiMap(project, plugins, log, {
+    const result = getPluginApiMap(project, plugins, plugins, log, {
       collectReferences: false,
       pluginFilter: ['pluginA'],
     });
@@ -111,7 +111,7 @@ describe('getPluginApiMap', () => {
     const pluginA = getKibanaPlatformPlugin('pluginA');
     const plugins = [pluginA];
 
-    const result = getPluginApiMap(project, plugins, log, {
+    const result = getPluginApiMap(project, plugins, plugins, log, {
       collectReferences: true,
     });
 
@@ -124,7 +124,7 @@ describe('getPluginApiMap', () => {
   });
 
   it('handles empty plugin list', () => {
-    const result = getPluginApiMap(project, [], log, {
+    const result = getPluginApiMap(project, [], [], log, {
       collectReferences: false,
     });
 
diff --git a/packages/kbn-docs-utils/src/get_plugin_api_map.ts b/packages/kbn-docs-utils/src/get_plugin_api_map.ts
index 9cd53f1d0f960..4e6a4a7870591 100644
--- a/packages/kbn-docs-utils/src/get_plugin_api_map.ts
+++ b/packages/kbn-docs-utils/src/get_plugin_api_map.ts
@@ -26,6 +26,7 @@ import type { AdoptionTrackedAPIStats } from './types';
 export function getPluginApiMap(
   project: Project,
   plugins: PluginOrPackage[],
+  allPlugins: PluginOrPackage[],
   log: ToolingLog,
   { collectReferences, pluginFilter }: { collectReferences: boolean; pluginFilter?: string[] }
 ): {
@@ -43,7 +44,15 @@ export function getPluginApiMap(
   plugins.forEach((plugin) => {
     const captureReferences =
       collectReferences && (!pluginFilter || pluginFilter.indexOf(plugin.id) >= 0);
-    const { pluginApi, warnings } = getPluginApi(project, plugin, plugins, log, captureReferences);
+
+    // Pass allPlugins for cross-reference resolution (links to other packages)
+    const { pluginApi, warnings } = getPluginApi(
+      project,
+      plugin,
+      allPlugins,
+      log,
+      captureReferences
+    );
     pluginApiMap[plugin.id] = pluginApi;
     if (warnings.unnamedExports.length > 0) {
       unnamedExports[plugin.id] = warnings.unnamedExports;
diff --git a/packages/kbn-docs-utils/src/integration_tests/api_doc_suite.test.ts b/packages/kbn-docs-utils/src/integration_tests/api_doc_suite.test.ts
index 31002079f1d2a..6ca3e29dad00b 100644
--- a/packages/kbn-docs-utils/src/integration_tests/api_doc_suite.test.ts
+++ b/packages/kbn-docs-utils/src/integration_tests/api_doc_suite.test.ts
@@ -125,7 +125,7 @@ beforeAll(async () => {
     referencedDeprecations,
     adoptionTrackedAPIs,
     unnamedExports,
-  } = getPluginApiMap(project, plugins, log, { collectReferences: false });
+  } = getPluginApiMap(project, plugins, plugins, log, { collectReferences: false });
 
   doc = pluginApiMap.pluginA;
 
diff --git a/packages/kbn-docs-utils/src/utils.ts b/packages/kbn-docs-utils/src/utils.ts
index c80c6371c0c6d..c50cc2ed2e3dc 100644
--- a/packages/kbn-docs-utils/src/utils.ts
+++ b/packages/kbn-docs-utils/src/utils.ts
@@ -194,9 +194,9 @@ export function removeBrokenLinks(
 
   const uniqueMissing = Object.keys(missingApiItems[pluginApi.id] ?? {}).length;
 
-  if (uniqueMissing > 0) {
+  if (missingCnt > 0) {
     log.info(
-      `${pluginApi.id} had ${uniqueMissing} missing exported API item(s). Removed ${missingCnt} reference(s) to avoid broken links. Use '--stats exports' to list missing exports.`
+      `${pluginApi.id}: removed ${missingCnt} broken link(s) referencing ${uniqueMissing} unexported API item(s). Run 'check_package_docs --check exports' for details.`
     );
   }
 }
@@ -211,7 +211,16 @@ function removeBrokenLinksFromApi(
   if (api.signature) {
     api.signature = api.signature.map((sig) => {
       if (typeof sig !== 'string') {
-        if (!apiItemExists(sig.text, sig.scope, pluginApiMap[sig.pluginId])) {
+        const referencedPluginApi = pluginApiMap[sig.pluginId];
+
+        // If the referenced plugin isn't in our plugin map (e.g., single-package build),
+        // keep the link as-is since we can't verify if it exists.
+        if (!referencedPluginApi) {
+          return sig;
+        }
+
+        // Plugin is in the map - check if the specific API item exists.
+        if (!apiItemExists(sig.text, sig.scope, referencedPluginApi)) {
           if (missingApiItems[sig.pluginId] === undefined) {
             missingApiItems[sig.pluginId] = {};
           }
@@ -223,6 +232,7 @@ function removeBrokenLinksFromApi(
           missingApiItems[sig.pluginId][sourceId].push(`${pluginId}-${api.id}`);
 
           missingCnt++;
+          // Return plain text for broken links.
           return sig.text;
         }
         return sig;