diff --git a/packages/metro-file-map/src/plugins/MockPlugin.js b/packages/metro-file-map/src/plugins/MockPlugin.js
index 805c0c5bb1..98e119f744 100644
--- a/packages/metro-file-map/src/plugins/MockPlugin.js
+++ b/packages/metro-file-map/src/plugins/MockPlugin.js
@@ -147,13 +147,18 @@ export default class MockPlugin
     const duplicates = this.#raw.duplicates.get(mockName);
     if (duplicates != null) {
       const posixRelativePath = normalizePathSeparatorsToPosix(canonicalPath);
+      const wasActiveMock = this.#raw.mocks.get(mockName) === posixRelativePath;
       duplicates.delete(posixRelativePath);
       if (duplicates.size === 1) {
         this.#raw.duplicates.delete(mockName);
       }
-      // Set the mock to a remaining duplicate. Should never be empty.
-      const remaining = nullthrows(duplicates.values().next().value);
-      this.#raw.mocks.set(mockName, remaining);
+      // Only reassign the active mock if the file we removed *was* the active
+      // one; otherwise a non-active duplicate's removal would clobber it.
+      if (wasActiveMock) {
+        // Set the mock to a remaining duplicate. Should never be empty.
+        const remaining = nullthrows(duplicates.values().next().value);
+        this.#raw.mocks.set(mockName, remaining);
+      }
     } else {
       this.#raw.mocks.delete(mockName);
     }
diff --git a/packages/metro-file-map/src/plugins/mocks/__tests__/MockPlugin-test.js b/packages/metro-file-map/src/plugins/mocks/__tests__/MockPlugin-test.js
index 43f2835646..36e95abf24 100644
--- a/packages/metro-file-map/src/plugins/mocks/__tests__/MockPlugin-test.js
+++ b/packages/metro-file-map/src/plugins/mocks/__tests__/MockPlugin-test.js
@@ -107,6 +107,25 @@ Duplicate manual mock found for \`foo\`:
     });
   });
 
+  test('removing a non-active duplicate keeps the active mock', () => {
+    onFileAdded(p('a/__mocks__/foo.js'));
+    onFileAdded(p('b/__mocks__/foo.js'));
+    onFileAdded(p('c/__mocks__/foo.js')); // latest wins -> active mock is c
+
+    expect(mockMap.getMockModule('foo')).toBe(p('/root/c/__mocks__/foo.js'));
+
+    // Remove a NON-active duplicate (b); the active mock (c) must be kept.
+    mockMap.onChanged({
+      addedFiles: new Map(),
+      modifiedFiles: new Map(),
+      removedFiles: new Map([[p('b/__mocks__/foo.js'), null]]),
+      addedDirectories: new Set(),
+      removedDirectories: new Set(),
+    });
+
+    expect(mockMap.getMockModule('foo')).toBe(p('/root/c/__mocks__/foo.js'));
+  });
+
   test('loads from a snapshot', async () => {
     await mockMap.initialize({
       files: {