diff --git a/lib/helpers/schema/merge.js b/lib/helpers/schema/merge.js
index edc5175eedc..55ed82466f7 100644
--- a/lib/helpers/schema/merge.js
+++ b/lib/helpers/schema/merge.js
@@ -23,5 +23,6 @@ module.exports = function merge(s1, s2, skipConflictingPaths) {
     s1.virtuals[virtual] = s2.virtuals[virtual].clone();
   }
 
+  s1._indexes = s1._indexes.concat(s2._indexes || []);
   s1.s.hooks.merge(s2.s.hooks, false);
 };
diff --git a/test/schema.test.js b/test/schema.test.js
index d2bff3ce34e..cdaed581759 100644
--- a/test/schema.test.js
+++ b/test/schema.test.js
@@ -2401,6 +2401,16 @@ describe('schema', function() {
     assert.equal(TurboManSchema.path('year').instance, 'Number');
   });
 
+  it('copies indexes when calling add() with schema instance (gh-12654)', function() {
+    const ToySchema = Schema({ name: String });
+    ToySchema.index({ name: 1 });
+
+    const TurboManSchema = Schema();
+    TurboManSchema.add(ToySchema);
+
+    assert.deepStrictEqual(TurboManSchema.indexes(), [[{ name: 1 }, { background: true }]]);
+  });
+
   describe('gh-8849', function() {
     it('treats `select: undefined` as not specifying `select` option', function() {
       const userSchema = new Schema({ name: { type: String, select: undefined } });