diff --git a/packages/platform-api-docs/CHANGELOG.md b/packages/platform-api-docs/CHANGELOG.md
index 6e3cfcc96a..9ffd3bba8e 100644
--- a/packages/platform-api-docs/CHANGELOG.md
+++ b/packages/platform-api-docs/CHANGELOG.md
@@ -12,6 +12,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Speed up documentation generation by loading source files in bulk instead of one at a time ([#9990](https://github.com/MetaMask/core/pull/9990))
 - Bump `@metamask/utils` from `^11.11.0` to `^11.12.0` ([#10076](https://github.com/MetaMask/core/pull/10076))
 
+### Fixed
+
+- Link a capability to its source rather than to the build output compiled from it, where both are available ([#10085](https://github.com/MetaMask/core/pull/10085))
+
 ## [0.1.0]
 
 ### Added
diff --git a/packages/platform-api-docs/src/generate.test.ts b/packages/platform-api-docs/src/generate.test.ts
index fa284232fc..e1971a9c6e 100644
--- a/packages/platform-api-docs/src/generate.test.ts
+++ b/packages/platform-api-docs/src/generate.test.ts
@@ -338,6 +338,77 @@ export type FooMessenger = Messenger<'Foo', FooAction, never>;
     });
   });
 
+  it('deduplicates items preferring source over build output', async () => {
+    expect.assertions(2);
+
+    await withinSandbox(async ({ directoryPath }) => {
+      // Reproduces how build output wins in a real monorepo. `a-controller` is
+      // scanned before `b-controller`, and its import of `@metamask/b-controller`
+      // resolves through node_modules to the published `.d.cts`, so the first
+      // declaration seen for `B:get` is the built one. The source declaration is
+      // reached later, when `b-controller/src` is scanned, and should win.
+      const declaration = `
+/** Gets b. */
+export type BGetAction = {
+  type: 'B:get';
+  handler: () => string;
+};
+`;
+
+      const bSrc = path.join(directoryPath, 'packages', 'b-controller', 'src');
+      await fs.promises.mkdir(bSrc, { recursive: true });
+      await fs.promises.writeFile(
+        path.join(bSrc, 'BController.ts'),
+        `${declaration}
+export type BMessenger = Messenger<'B', BGetAction, never>;
+`,
+      );
+
+      const bDist = path.join(
+        directoryPath,
+        'node_modules',
+        '@metamask',
+        'b-controller',
+        'dist',
+      );
+      await fs.promises.mkdir(bDist, { recursive: true });
+      await fs.promises.writeFile(path.join(bDist, 'index.d.cts'), declaration);
+      await fs.promises.writeFile(
+        path.join(bDist, '..', 'package.json'),
+        JSON.stringify({
+          name: '@metamask/b-controller',
+          types: './dist/index.d.cts',
+        }),
+      );
+
+      const aSrc = path.join(directoryPath, 'packages', 'a-controller', 'src');
+      await fs.promises.mkdir(aSrc, { recursive: true });
+      await fs.promises.writeFile(
+        path.join(aSrc, 'AController.ts'),
+        `
+import type { BGetAction } from '@metamask/b-controller';
+
+export type AMessenger = Messenger<'A', BGetAction, never>;
+`,
+      );
+
+      const outputDir = path.join(directoryPath, '.docs');
+      await generate({
+        projectPath: directoryPath,
+        outputDir,
+        strategy: 'scan',
+        scanDirs: ['src'],
+      });
+
+      const actionsMd = await fs.promises.readFile(
+        path.join(outputDir, 'docs', 'B', 'actions.md'),
+        'utf8',
+      );
+      expect(actionsMd).toContain('packages/b-controller/src/BController.ts');
+      expect(actionsMd).not.toContain('/dist/');
+    });
+  });
+
   it('returns zero counts for project with no messenger types', async () => {
     expect.assertions(3);
 
diff --git a/packages/platform-api-docs/src/generate.ts b/packages/platform-api-docs/src/generate.ts
index 61e7ecdf7c..773be71690 100644
--- a/packages/platform-api-docs/src/generate.ts
+++ b/packages/platform-api-docs/src/generate.ts
@@ -105,7 +105,14 @@ function deduplicationScore(item: MessengerCapabilityPacket): number {
     item.sourceFile.toLowerCase().includes(namespacePrefix)
       ? 1
       : 0;
-  return jsDocScore + homeScore;
+  // A capability declared in a package's own source is usually also visible in
+  // the `dist` built from it, and a cross-package import resolves to that
+  // `dist` rather than to the sibling's source. Prefer the source, which is
+  // what an engineer can actually read and edit. Projects that only ever see
+  // published packages score every candidate the same way, so nothing changes
+  // for them.
+  const sourceScore = /[\\/]dist[\\/]/u.test(item.sourceFile) ? 0 : 1;
+  return jsDocScore + homeScore + sourceScore;
 }
 
 const execFileAsync = promisify(execFile);
@@ -353,16 +360,11 @@ async function scanSources(
   sources: ScanSources,
 ): Promise<MessengerCapabilityPacket[]> {
   const project = createProject();
-  const sourceFiles = [];
+  const patterns: string[] = [];
 
   for (const dir of sources.scanDirs) {
     const root = await toGlobPath(projectPath, dir);
-    sourceFiles.push(
-      ...addSourceFiles(project, [
-        `${root}/**/*.ts`,
-        ...buildTsSourceExclusions(root),
-      ]),
-    );
+    patterns.push(`${root}/**/*.ts`, ...buildTsSourceExclusions(root));
   }
 
   if (sources.packagesDir) {
@@ -370,19 +372,19 @@ async function scanSources(
     // Anchored at each package's `src`, not at `packages` itself, so a package
     // whose name collides with an exclusion (`test`, `dist`) isn't dropped.
     const contentRoot = `${root}/*/src`;
-    sourceFiles.push(
-      ...addSourceFiles(project, [
-        `${contentRoot}/**/*.ts`,
-        ...buildTsSourceExclusions(contentRoot),
-      ]),
+    patterns.push(
+      `${contentRoot}/**/*.ts`,
+      ...buildTsSourceExclusions(contentRoot),
     );
   }
 
   if (sources.nodeModulesDir) {
     const root = await toGlobPath(sources.nodeModulesDir);
-    sourceFiles.push(...addSourceFiles(project, [`${root}/*/dist/**/*.d.cts`]));
+    patterns.push(`${root}/*/dist/**/*.d.cts`);
   }
 
+  const sourceFiles = addSourceFiles(project, patterns);
+
   // Matched paths are fully resolved, so the root they are made relative to
   // has to be resolved the same way or every source link becomes a `../..`
   // walk out of the project.