diff --git a/packages/cli-platform-android/src/config/__fixtures__/android.ts b/packages/cli-platform-android/src/config/__fixtures__/android.ts
index c187e0a62..44c2b8f39 100644
--- a/packages/cli-platform-android/src/config/__fixtures__/android.ts
+++ b/packages/cli-platform-android/src/config/__fixtures__/android.ts
@@ -30,6 +30,14 @@ const classNameManifest = fs.readFileSync(
   path.join(__dirname, './files/AndroidManifest-className.xml'),
 );
 
+const customFlavorManifest = fs.readFileSync(
+  path.join(__dirname, './files/AndroidManifest-custom-flavor.xml'),
+);
+
+const mainManifest = fs.readFileSync(
+  path.join(__dirname, './files/AndroidManifest.xml'),
+);
+
 function generateValidFileStructureForLib(classFileName: string) {
   return {
     'build.gradle': buildGradle,
@@ -298,3 +306,14 @@ export const className = {
     'AndroidManifest.xml': classNameManifest,
   },
 };
+
+export const customFlavor = {
+  src: {
+    e2e: {
+      'AndroidManifest.xml': customFlavorManifest,
+    },
+    main: {
+      'AndroidManifest.xml': mainManifest,
+    },
+  },
+};
diff --git a/packages/cli-platform-android/src/config/__fixtures__/files/AndroidManifest-custom-flavor.xml b/packages/cli-platform-android/src/config/__fixtures__/files/AndroidManifest-custom-flavor.xml
new file mode 100644
index 000000000..0c29eab67
--- /dev/null
+++ b/packages/cli-platform-android/src/config/__fixtures__/files/AndroidManifest-custom-flavor.xml
@@ -0,0 +1,3 @@
+<manifest
+  xmlns:android="http://schemas.android.com/apk/res/android">
+</manifest>
diff --git a/packages/cli-platform-android/src/config/__tests__/getMainActivity.test.ts b/packages/cli-platform-android/src/config/__tests__/getMainActivity.test.ts
index 9b7bc190a..a1acfed78 100644
--- a/packages/cli-platform-android/src/config/__tests__/getMainActivity.test.ts
+++ b/packages/cli-platform-android/src/config/__tests__/getMainActivity.test.ts
@@ -26,6 +26,11 @@ describe('android::getMainActivity', () => {
           app: mocks.fewActivities,
         },
       },
+      customFlavor: {
+        android: {
+          app: mocks.customFlavor,
+        },
+      },
     });
   });
 
@@ -53,6 +58,14 @@ describe('android::getMainActivity', () => {
     expect(mainActivity).toBe('com.example.ExampleAppActivity');
   });
 
+  it('returns main activity from main manifest when custom flavors are defined', () => {
+    const manifestPath = findManifest('/customFlavor');
+    const mainActivity = getMainActivity(manifestPath || '');
+    expect(mainActivity).not.toBeNull();
+    expect(typeof mainActivity).toBe('string');
+    expect(mainActivity).toBe('.MainActivity');
+  });
+
   it('returns null if file do not exist', () => {
     const fakeManifestPath = findManifest('/empty');
     expect(getMainActivity(fakeManifestPath || '')).toBeNull();
diff --git a/packages/cli-platform-android/src/config/findManifest.ts b/packages/cli-platform-android/src/config/findManifest.ts
index 68292fe2e..9955d47d0 100644
--- a/packages/cli-platform-android/src/config/findManifest.ts
+++ b/packages/cli-platform-android/src/config/findManifest.ts
@@ -10,7 +10,7 @@ import glob from 'glob';
 import path from 'path';
 
 export default function findManifest(folder: string) {
-  const manifestPath = glob.sync(path.join('**', 'AndroidManifest.xml'), {
+  let manifestPaths = glob.sync(path.join('**', 'AndroidManifest.xml'), {
     cwd: folder,
     ignore: [
       'node_modules/**',
@@ -23,7 +23,16 @@ export default function findManifest(folder: string) {
       '**/src/androidTest/**',
       '**/src/test/**',
     ],
-  })[0];
+  });
+  if (manifestPaths.length > 1) {
+    // if we have more than one manifest, pick the one in the main folder if present
+    const mainManifest = manifestPaths.filter((manifestPath) =>
+      manifestPath.includes('src/main/'),
+    );
+    if (mainManifest.length === 1) {
+      manifestPaths = mainManifest;
+    }
+  }
 
-  return manifestPath ? path.join(folder, manifestPath) : null;
+  return manifestPaths[0] ? path.join(folder, manifestPaths[0]) : null;
 }