diff --git a/lib/query.js b/lib/query.js
index 61c15f44419..30e85f7985b 100644
--- a/lib/query.js
+++ b/lib/query.js
@@ -2402,6 +2402,10 @@ Query.prototype.merge = function(source) {
 
     utils.merge(this._mongooseOptions, source._mongooseOptions);
 
+    return this;
+  } else if (this.model != null && source instanceof this.model.base.Types.ObjectId) {
+    utils.merge(this._conditions, { _id: source }, opts);
+
     return this;
   }
 
diff --git a/test/helpers/update.castArrayFilters.test.js b/test/helpers/update.castArrayFilters.test.js
index c4a7420010b..6baad3f8474 100644
--- a/test/helpers/update.castArrayFilters.test.js
+++ b/test/helpers/update.castArrayFilters.test.js
@@ -2,6 +2,7 @@
 
 const Query = require('../../lib/query');
 const Schema = require('../../lib/schema');
+const Types = require('../../lib/types');
 const assert = require('assert');
 const castArrayFilters = require('../../lib/helpers/update/castArrayFilters');
 
@@ -231,7 +232,7 @@ describe('castArrayFilters', function() {
     });
     let q = new Query();
     q.schema = schema;
-    q.model = { base: { options: { strictQuery: false } } };
+    q.model = { base: { Types, options: { strictQuery: false } } };
 
     let p = { 'arr.$[arr].id': 42 };
     let opts = {
@@ -247,7 +248,7 @@ describe('castArrayFilters', function() {
 
     q = new Query();
     q.schema = schema;
-    q.model = { base: { options: { strictQuery: true } } };
+    q.model = { base: { Types, options: { strictQuery: true } } };
 
     p = { 'arr.$[arr].id': 42 };
     opts = {
diff --git a/test/query.test.js b/test/query.test.js
index 59698e99fdb..0b3a6af2339 100644
--- a/test/query.test.js
+++ b/test/query.test.js
@@ -4132,4 +4132,20 @@ describe('Query', function() {
     assert.equal(item.get('select.key.some'), 'value');
     assert.equal(item.doNotSelect, undefined);
   });
+
+  it('treats ObjectId as object with `_id` for `merge()` (gh-12325)', async function() {
+    const testSchema = new mongoose.Schema({ name: String });
+    const Test = db.model('Test', testSchema);
+    const _id = new mongoose.Types.ObjectId();
+
+    let q = Test.find(_id);
+
+    assert.ok(q.getFilter()._id instanceof mongoose.Types.ObjectId);
+    assert.equal(q.getFilter()._id.toHexString(), _id.toHexString());
+
+    q = Test.findOne(_id);
+
+    assert.ok(q.getFilter()._id instanceof mongoose.Types.ObjectId);
+    assert.equal(q.getFilter()._id.toHexString(), _id.toHexString());
+  });
 });