diff --git a/lib/helpers/populate/assignVals.js b/lib/helpers/populate/assignVals.js
index 651a48e4887..da40f396e2a 100644
--- a/lib/helpers/populate/assignVals.js
+++ b/lib/helpers/populate/assignVals.js
@@ -52,6 +52,11 @@ module.exports = function assignVals(o) {
 
     const _allIds = o.allIds[i];
 
+    if (o.path.endsWith('.$*')) {
+      // Skip maps re: gh-12494
+      return valueFilter(val, options, populateOptions, _allIds);
+    }
+
     if (o.justOne === true && Array.isArray(val)) {
       // Might be an embedded discriminator (re: gh-9244) with multiple models, so make sure to pick the right
       // model before assigning.
diff --git a/lib/types/map.js b/lib/types/map.js
index 3c68026fa0e..6516d2e4038 100644
--- a/lib/types/map.js
+++ b/lib/types/map.js
@@ -97,15 +97,27 @@ class MongooseMap extends Map {
 
     const fullPath = this.$__path + '.' + key;
     const populated = this.$__parent != null && this.$__parent.$__ ?
-      this.$__parent.$populated(fullPath) || this.$__parent.$populated(this.$__path) :
+      this.$__parent.$populated(fullPath, true) || this.$__parent.$populated(this.$__path, true) :
       null;
     const priorVal = this.get(key);
 
     if (populated != null) {
-      if (value.$__ == null) {
-        value = new populated.options[populateModelSymbol](value);
+      if (Array.isArray(value) && this.$__schemaType.$isMongooseArray) {
+        value = value.map(v => {
+          if (v.$__ == null) {
+            v = new populated.options[populateModelSymbol](v);
+          }
+          // Doesn't support single nested "in-place" populate
+          v.$__.wasPopulated = { value: v._id };
+          return v;
+        });
+      } else {
+        if (value.$__ == null) {
+          value = new populated.options[populateModelSymbol](value);
+        }
+        // Doesn't support single nested "in-place" populate
+        value.$__.wasPopulated = { value: value._id };
       }
-      value.$__.wasPopulated = { value: populated.value };
     } else {
       try {
         value = this.$__schemaType.
diff --git a/test/types.map.test.js b/test/types.map.test.js
index 9edd721b068..c3415a6c3bf 100644
--- a/test/types.map.test.js
+++ b/test/types.map.test.js
@@ -1050,4 +1050,45 @@ describe('Map', function() {
     const res = doc.toObject({ flattenMaps: true });
     assert.equal(res.l1.l1key.l2.l2key.value, 'abc');
   });
+
+  it('handles populating map of arrays (gh-12494)', async function() {
+    const User = new mongoose.Schema({
+      name: String,
+      addresses: {
+        type: Map,
+        of: [{
+          type: mongoose.Schema.Types.ObjectId,
+          ref: 'Address'
+        }],
+        default: {}
+      }
+    });
+
+    const Address = new mongoose.Schema({
+      city: String
+    });
+
+    const UserModel = db.model('User', User);
+    const AddressModel = db.model('Address', Address);
+
+    const address = await new AddressModel({ city: 'London' }).save();
+
+    const { _id } = await new UserModel({
+      name: 'Name',
+      addresses: {
+        home: [address._id]
+      }
+    }).save();
+
+    const query = UserModel.findById(_id);
+
+    query.populate({
+      path: 'addresses.$*'
+    });
+
+    const doc = await query.exec();
+    assert.ok(Array.isArray(doc.addresses.get('home')));
+    assert.equal(doc.addresses.get('home').length, 1);
+    assert.equal(doc.addresses.get('home')[0].city, 'London');
+  });
 });