diff --git a/code/core/src/core-server/utils/StoryIndexGenerator.test.ts b/code/core/src/core-server/utils/StoryIndexGenerator.test.ts
index 6692ea1881b4..ea3bfc2d51c8 100644
--- a/code/core/src/core-server/utils/StoryIndexGenerator.test.ts
+++ b/code/core/src/core-server/utils/StoryIndexGenerator.test.ts
@@ -1956,6 +1956,31 @@ describe('StoryIndexGenerator', () => {
           }
         `);
       });
+
+      it('puts the Meta of stories file first in storiesImports even when it is not the last import', async () => {
+        const csfSpecifier: NormalizedStoriesSpecifier = normalizeStoriesEntry(
+          './src/*.stories.(js|ts)',
+          options
+        );
+
+        const docsSpecifier: NormalizedStoriesSpecifier = normalizeStoriesEntry(
+          './complex/MetaOfImportOrder.mdx',
+          options
+        );
+
+        const generator = new StoryIndexGenerator([csfSpecifier, docsSpecifier], options);
+        await generator.initialize();
+
+        const { storyIndex } = await generator.getIndexAndStats();
+        const docsEntry = storyIndex.entries['a--metaofimportorder'];
+
+        expect(docsEntry).toMatchObject({
+          type: 'docs',
+          title: 'A',
+          importPath: './complex/MetaOfImportOrder.mdx',
+          storiesImports: ['./src/A.stories.js', './src/B.stories.ts'],
+        });
+      });
     });
 
     describe('errors', () => {
diff --git a/code/core/src/core-server/utils/StoryIndexGenerator.ts b/code/core/src/core-server/utils/StoryIndexGenerator.ts
index 11a7b9d4981a..6882ffdce05e 100644
--- a/code/core/src/core-server/utils/StoryIndexGenerator.ts
+++ b/code/core/src/core-server/utils/StoryIndexGenerator.ts
@@ -553,6 +553,8 @@ export class StoryIndexGenerator {
       let csfEntry: StoryIndexEntryWithExtra | undefined;
       if (result.of) {
         const absoluteOf = makeAbsolute(result.of, normalizedPath, this.options.workingDir);
+        let metaDependency: StoriesCacheEntry | undefined;
+
         dependencies.forEach((dep) => {
           if (dep.entries.length > 0) {
             const first = dep.entries.find((e) => e.type !== 'docs') as StoryIndexEntryWithExtra;
@@ -563,12 +565,18 @@ export class StoryIndexGenerator {
               )
             ) {
               csfEntry = first;
+              metaDependency = dep;
             }
           }
-
-          sortedDependencies = [dep, ...dependencies.filter((d) => d !== dep)];
         });
 
+        if (metaDependency) {
+          sortedDependencies = [
+            metaDependency,
+            ...dependencies.filter((d) => d !== metaDependency),
+          ];
+        }
+
         invariant(
           csfEntry,
           dedent`
diff --git a/code/core/src/core-server/utils/__mockdata__/complex/MetaOfImportOrder.mdx b/code/core/src/core-server/utils/__mockdata__/complex/MetaOfImportOrder.mdx
new file mode 100644
index 000000000000..2774c1863d95
--- /dev/null
+++ b/code/core/src/core-server/utils/__mockdata__/complex/MetaOfImportOrder.mdx
@@ -0,0 +1,9 @@
+{/* References BStories first, but is attached to A */}
+import * as BStories from '../src/B.stories';
+import * as AStories from '../src/A.stories';
+
+<Meta of={AStories}/>
+
+# This file references two story files
+
+It is important that A.stories is the first listed in `storiesImports` even when it is not the first import.
\ No newline at end of file
diff --git a/code/renderers/react/src/componentManifest/generator.test.ts b/code/renderers/react/src/componentManifest/generator.test.ts
index a9140d47e4b1..71473530eab5 100644
--- a/code/renderers/react/src/componentManifest/generator.test.ts
+++ b/code/renderers/react/src/componentManifest/generator.test.ts
@@ -578,6 +578,101 @@ test('should create component manifest when only attached-mdx docs have manifest
   `);
 });
 
+test('should prefer story entries over attached-mdx docs entries for the same component id', async () => {
+  vol.fromJSON(
+    {
+      ['./package.json']: JSON.stringify({ name: 'some-package' }),
+      ['./src/Primary/Primary.stories.tsx']: dedent`
+        import type { Meta } from '@storybook/react';
+        import { Primary } from './Primary';
+
+        const meta = {
+          title: 'Example/Primary',
+          component: Primary,
+        } satisfies Meta<typeof Primary>;
+        export default meta;
+
+        export const Default = () => <Primary title="Primary title" />;
+      `,
+      ['./src/Primary/Primary.tsx']: dedent`
+        import React from 'react';
+
+        export interface PrimaryProps {
+          title: string;
+        }
+
+        /** Primary component description */
+        export const Primary = ({ title }: PrimaryProps) => <div>{title}</div>;
+      `,
+      ['./src/OtherFile/OtherFile.stories.tsx']: dedent`
+        import type { Meta } from '@storybook/react';
+        import { OtherFile } from './OtherFile';
+
+        const meta = {
+          title: 'Example/Other File',
+          component: OtherFile,
+        } satisfies Meta<typeof OtherFile>;
+        export default meta;
+
+        export const Default = () => <OtherFile label="Other file label" />;
+      `,
+      ['./src/OtherFile/OtherFile.tsx']: dedent`
+        import React from 'react';
+
+        export interface OtherFileProps {
+          label: string;
+        }
+
+        /** Other file component description */
+        export const OtherFile = ({ label }: OtherFileProps) => (
+          <button type="button">{label}</button>
+        );
+      `,
+    },
+    '/app'
+  );
+
+  const manifestEntries = [
+    {
+      type: 'docs',
+      id: 'example-primary--docs',
+      name: 'Docs',
+      title: 'Example/Primary',
+      importPath: './src/Primary/Primary.mdx',
+      tags: [Tag.DEV, Tag.TEST, Tag.MANIFEST, Tag.ATTACHED_MDX],
+      storiesImports: [
+        './src/OtherFile/OtherFile.stories.tsx',
+        './src/Primary/Primary.stories.tsx',
+      ],
+    },
+    {
+      type: 'story',
+      subtype: 'story',
+      id: 'example-primary--default',
+      name: 'Default',
+      title: 'Example/Primary',
+      importPath: './src/Primary/Primary.stories.tsx',
+      componentPath: './src/Primary/Primary.tsx',
+      tags: [Tag.DEV, Tag.TEST, Tag.MANIFEST],
+      exportName: 'Default',
+    },
+  ];
+
+  const result = await manifests(undefined, { manifestEntries } as any);
+
+  const component = result?.components?.components?.['example-primary'];
+
+  expect(component?.name).toBe('Primary');
+  expect(component?.path).toBe('./src/Primary/Primary.stories.tsx');
+  expect(component?.stories).toMatchObject([
+    {
+      id: 'example-primary--default',
+      name: 'Default',
+    },
+  ]);
+  expect(component?.stories[0]?.snippet).toContain('<Primary');
+});
+
 test('stories are populated when meta has no explicit title', async () => {
   vol.fromJSON(
     {
diff --git a/code/renderers/react/src/componentManifest/generator.ts b/code/renderers/react/src/componentManifest/generator.ts
index cab8ceea09f2..2c613863c048 100644
--- a/code/renderers/react/src/componentManifest/generator.ts
+++ b/code/renderers/react/src/componentManifest/generator.ts
@@ -9,7 +9,6 @@ import {
   type StorybookConfigRaw,
 } from 'storybook/internal/types';
 
-import { uniqBy } from 'es-toolkit/array';
 import path from 'pathe';
 
 import { getCodeSnippet } from './generateCodeSnippet';
@@ -24,6 +23,41 @@ interface ReactComponentManifest extends ComponentManifest {
   reactDocgenTypescript?: ComponentDocWithExportName;
 }
 
+function selectComponentEntries(manifestEntries: IndexEntry[]) {
+  const entriesByComponentId = new Map<string, IndexEntry>();
+
+  manifestEntries
+    .filter(
+      (entry) =>
+        (entry.type === 'story' && entry.subtype === 'story') ||
+        // Attached docs entries are the only docs entries that can contribute to a
+        // component manifest, because they point back to a story file through storiesImports.
+        (entry.type === 'docs' &&
+          entry.tags?.includes(Tag.ATTACHED_MDX) &&
+          entry.storiesImports.length > 0)
+    )
+    .forEach((entry) => {
+      const componentId = entry.id.split('--')[0];
+      const existingEntry = entriesByComponentId.get(componentId);
+
+      if (!existingEntry) {
+        // Keep the first eligible entry as a fallback so docs-only manifest coverage
+        // continues to work when no story entry for that component carries the manifest tag.
+        entriesByComponentId.set(componentId, entry);
+        return;
+      }
+
+      if (existingEntry.type === 'docs' && entry.type === 'story') {
+        // When both entries exist for the same component id, the story entry is authoritative.
+        // Attached docs may list unrelated stories first in storiesImports, so using the story
+        // entry avoids resolving the manifest from the wrong file.
+        entriesByComponentId.set(componentId, entry);
+      }
+    });
+
+  return [...entriesByComponentId.values()];
+}
+
 function findMatchingComponent(
   components: ReturnType<typeof getComponents>,
   componentName: string | undefined,
@@ -114,18 +148,7 @@ export const manifests: PresetPropertyFn<
 
   const startTime = performance.now();
 
-  const entriesByUniqueComponent = uniqBy(
-    manifestEntries.filter(
-      (entry) =>
-        (entry.type === 'story' && entry.subtype === 'story') ||
-        // addon-docs will add docs entries to these manifest entries afterwards
-        // Docs entries have importPath pointing to MDX file, but storiesImports[0] points to the story file
-        (entry.type === 'docs' &&
-          entry.tags?.includes(Tag.ATTACHED_MDX) &&
-          entry.storiesImports.length > 0)
-    ),
-    (entry) => entry.id.split('--')[0]
-  );
+  const entriesByUniqueComponent = selectComponentEntries(manifestEntries);
 
   const components = entriesByUniqueComponent
     .map((entry): ReactComponentManifest | undefined => {