diff --git a/.changeset/true-buses-juggle.md b/.changeset/true-buses-juggle.md
new file mode 100644
index 00000000000..8eba7e4b09e
--- /dev/null
+++ b/.changeset/true-buses-juggle.md
@@ -0,0 +1,5 @@
+---
+'@astrojs/starlight': patch
+---
+
+Fixes Starlight Markdown processing being potentially applied to files that should not be processed.
diff --git a/packages/starlight/__tests__/markdown-processor/markdown-process.test.ts b/packages/starlight/__tests__/markdown-processor/markdown-process.test.ts
new file mode 100644
index 00000000000..a68c6b26a8d
--- /dev/null
+++ b/packages/starlight/__tests__/markdown-processor/markdown-process.test.ts
@@ -0,0 +1,51 @@
+import { describe, expect, test } from 'vitest';
+import {
+	getMarkdownProcessorPaths,
+	shouldTransformPath,
+} from '../../integrations/markdown-process';
+import { createPluginTestOptions } from '../test-utils';
+
+const root = new URL('file:///path/to/project/');
+const srcDir = new URL('./src/', root);
+
+describe('getMarkdownProcessorPaths', () => {
+	test('returns allowed directory paths with trailing slashes', async () => {
+		const allowedPaths = await getAllowedPaths(['./src/content/comments']);
+
+		expect(allowedPaths).toEqual([
+			'/path/to/project/src/content/docs/',
+			'/path/to/project/src/content/comments/',
+		]);
+	});
+});
+
+describe('shouldTransformPath', () => {
+	const allowedPaths = [
+		'/path/to/project/src/content/docs/',
+		'/path/to/project/src/content/comments/',
+	];
+
+	test('transforms files in allowed paths', () => {
+		expect(shouldTransformPath('/path/to/project/src/content/docs/index.md', allowedPaths)).toBe(
+			true
+		);
+		expect(
+			shouldTransformPath('/path/to/project/src/content/comments/index.md', allowedPaths)
+		).toBe(true);
+	});
+
+	test('does not transform sibling paths sharing the same prefix of allowed paths', () => {
+		expect(
+			shouldTransformPath('/path/to/project/src/content/docs-test/index.md', allowedPaths)
+		).toBe(false);
+		expect(
+			shouldTransformPath('/path/to/project/src/content/comments-test/index.md', allowedPaths)
+		).toBe(false);
+	});
+});
+
+async function getAllowedPaths(processedDirs: string[] = []) {
+	const options = await createPluginTestOptions({ title: 'Test', markdown: { processedDirs } });
+
+	return getMarkdownProcessorPaths({ ...options, astroConfig: { root, srcDir } });
+}
diff --git a/packages/starlight/integrations/markdown-process.ts b/packages/starlight/integrations/markdown-process.ts
index 7ba9815e118..0b99c8cf0fc 100644
--- a/packages/starlight/integrations/markdown-process.ts
+++ b/packages/starlight/integrations/markdown-process.ts
@@ -2,6 +2,7 @@ import { resolve } from 'node:path';
 import { fileURLToPath } from 'node:url';
 import type { AstroConfig } from 'astro';
 import { resolveCollectionPath } from '../utils/collection-fs';
+import { ensureTrailingSlash } from '../utils/path';
 import type { HookParameters, StarlightConfig } from '../types';
 
 /**
@@ -21,10 +22,12 @@ export interface MarkdownProcessorPluginOptions {
  * utility to determine if a file should be transformed by a plugin or not.
  */
 export function getMarkdownProcessorPaths(options: MarkdownProcessorPluginOptions): string[] {
-	const paths = [normalizePath(resolveCollectionPath('docs', options.astroConfig.srcDir))];
+	const paths = [normalizeDirectoryPath(resolveCollectionPath('docs', options.astroConfig.srcDir))];
 
 	for (const processedDir of options.starlightConfig.markdown.processedDirs) {
-		paths.push(normalizePath(resolve(fileURLToPath(options.astroConfig.root), processedDir)));
+		paths.push(
+			normalizeDirectoryPath(resolve(fileURLToPath(options.astroConfig.root), processedDir))
+		);
 	}
 
 	return paths;
@@ -50,3 +53,12 @@ const backSlashRegex = /\\/g;
 function normalizePath(path: string) {
 	return path.replace(backSlashRegex, '/');
 }
+
+/**
+ * Allowed paths are directory prefixes compared with `startsWith()` in {@link shouldTransformPath},
+ * so we ensure they have a trailing slash to avoid matching sibling directories with the same
+ * prefix.
+ */
+function normalizeDirectoryPath(path: string) {
+	return ensureTrailingSlash(normalizePath(path));
+}