diff --git a/lib/document.js b/lib/document.js
index afc9e5ceacc..19298d05773 100644
--- a/lib/document.js
+++ b/lib/document.js
@@ -4774,7 +4774,23 @@ Document.prototype.depopulate = function(path) {
         continue;
       }
       delete populated[key];
-      utils.setValue(key, populatedIds, this._doc);
+      if (Array.isArray(populatedIds)) {
+        const arr = utils.getValue(key, this._doc);
+        if (arr.isMongooseArray) {
+          const rawArray = arr.__array;
+          for (let i = 0; i < rawArray.length; ++i) {
+            const subdoc = rawArray[i];
+            if (subdoc == null) {
+              continue;
+            }
+            rawArray[i] = subdoc instanceof Document ? subdoc._doc._id : subdoc._id;
+          }
+        } else {
+          utils.setValue(key, populatedIds, this._doc);
+        }
+      } else {
+        utils.setValue(key, populatedIds, this._doc);
+      }
     }
     return this;
   }
@@ -4787,7 +4803,23 @@ Document.prototype.depopulate = function(path) {
       delete this.$$populatedVirtuals[singlePath];
       delete this._doc[singlePath];
     } else if (populatedIds) {
-      utils.setValue(singlePath, populatedIds, this._doc);
+      if (Array.isArray(populatedIds)) {
+        const arr = utils.getValue(singlePath, this._doc);
+        if (arr.isMongooseArray) {
+          const rawArray = arr.__array;
+          for (let i = 0; i < rawArray.length; ++i) {
+            const subdoc = rawArray[i];
+            if (subdoc == null) {
+              continue;
+            }
+            rawArray[i] = subdoc instanceof Document ? subdoc._doc._id : subdoc._id;
+          }
+        } else {
+          utils.setValue(singlePath, populatedIds, this._doc);
+        }
+      } else {
+        utils.setValue(singlePath, populatedIds, this._doc);
+      }
     }
   }
   return this;
diff --git a/lib/types/array/methods/index.js b/lib/types/array/methods/index.js
index b79628cd4cd..cf31914bb7e 100644
--- a/lib/types/array/methods/index.js
+++ b/lib/types/array/methods/index.js
@@ -721,6 +721,7 @@ const methods = {
     }
 
     this._registerAtomic('$push', atomic);
+
     return ret;
   },
 
diff --git a/test/document.populate.test.js b/test/document.populate.test.js
index 37e8ce3f600..bbfbc1df99a 100644
--- a/test/document.populate.test.js
+++ b/test/document.populate.test.js
@@ -552,7 +552,7 @@ describe('document.populate', function() {
 
       const docs = await Person.create([{ name: 'Axl Rose' }, { name: 'Slash' }]);
 
-      const band = await Band.create({
+      let band = await Band.create({
         name: 'Guns N\' Roses',
         members: [docs[0]._id, docs[1]],
         lead: docs[0]._id
@@ -561,18 +561,44 @@ describe('document.populate', function() {
       await band.populate('members');
 
       assert.equal(band.members[0].name, 'Axl Rose');
+      assert.ok(band.members.isMongooseArray);
+      assert.ok(band.members.addToSet);
       band.depopulate('members');
       assert.ok(!band.members[0].name);
       assert.equal(band.members[0].toString(), docs[0]._id.toString());
       assert.equal(band.members[1].toString(), docs[1]._id.toString());
+      assert.ok(band.members.isMongooseArray);
+      assert.ok(band.members.addToSet);
+      assert.deepStrictEqual(band.getChanges(), {});
       assert.ok(!band.populated('members'));
       assert.ok(!band.populated('lead'));
-      await band.populate('lead');
 
+      await band.populate('lead');
       assert.equal(band.lead.name, 'Axl Rose');
       band.depopulate('lead');
       assert.ok(!band.lead.name);
+      assert.deepStrictEqual(band.getChanges(), {});
       assert.equal(band.lead.toString(), docs[0]._id.toString());
+
+      const newId = new mongoose.Types.ObjectId();
+      band.lead = newId;
+      assert.deepStrictEqual(band.getChanges(), { $set: { lead: newId } });
+
+      band = await Band.findById(band._id).orFail();
+      await band.populate('members');
+
+      assert.equal(band.members[0].name, 'Axl Rose');
+      assert.ok(band.members.isMongooseArray);
+      assert.ok(band.members.addToSet);
+      band.depopulate('members');
+      assert.ok(!band.members[0].name);
+      assert.equal(band.members[0].toString(), docs[0]._id.toString());
+      assert.equal(band.members[1].toString(), docs[1]._id.toString());
+      assert.ok(band.members.isMongooseArray);
+      assert.ok(band.members.addToSet);
+      assert.deepStrictEqual(band.getChanges(), {});
+      assert.ok(!band.populated('members'));
+      assert.ok(!band.populated('lead'));
     });
 
     it('depopulates all (gh-6073)', async function() {
@@ -706,7 +732,62 @@ describe('document.populate', function() {
       author.depopulate('books');
       assert.ok(author.books);
       assert.strictEqual(author.books.length, 0);
+    });
+
+    it('depopulates after pushing manually populated (gh-2509)', async function() {
+      const Book = db.model(
+        'Book',
+        new mongoose.Schema({
+          name: String,
+          chapters: Number
+        })
+      );
+      const Author = db.model(
+        'Person',
+        new mongoose.Schema({
+          name: String,
+          books: { type: [{ type: mongoose.Schema.Types.ObjectId, ref: 'Book' }], default: [] }
+        })
+      );
+
+      const books = await Book.create([
+        { name: 'Lost Years of Merlin' },
+        { name: 'Seven Songs of Merlin' },
+        { name: 'Fires of Merlin' }
+      ]);
+      let author = new Author({
+        name: 'T.A. Barron',
+        books: [books[0]._id]
+      });
+      await author.save();
+      await author.populate('books');
+      assert.ok(author.books);
+      assert.strictEqual(author.books.length, 1);
+
+      author.books.push(books[1]);
+      author.depopulate('books');
+      assert.ok(author.books);
+      assert.ok(author.books.isMongooseArray);
+      assert.ok(!author.$populated('books'));
+      assert.deepStrictEqual(author.books, [books[0]._id, books[1]._id]);
+      await author.save();
+
+      author = await Author.findById(author._id).orFail();
+      assert.strictEqual(author.books.length, 2);
+      assert.deepStrictEqual(author.books, [books[0]._id, books[1]._id]);
+      await author.populate('books');
+      author.books.pull(books[0]._id);
+      assert.strictEqual(author.books.length, 1);
+      assert.equal(author.books[0].name, 'Seven Songs of Merlin');
+      author.depopulate();
+      assert.ok(author.books);
+      assert.ok(author.books.isMongooseArray);
+      assert.deepStrictEqual(author.books, [books[1]._id]);
+      await author.save();
 
+      author = await Author.findById(author._id).orFail();
+      assert.strictEqual(author.books.length, 1);
+      assert.deepStrictEqual(author.books, [books[1]._id]);
     });
   });
 
diff --git a/test/document.test.js b/test/document.test.js
index f65479224d0..7158464a748 100644
--- a/test/document.test.js
+++ b/test/document.test.js
@@ -10805,7 +10805,10 @@ describe('document', function() {
     assert.ok(!band.populated('members'));
     assert.ok(!band.populated('lead'));
     assert.ok(!band.populated('embeddedMembers.member'));
+    assert.ok(band.members.isMongooseArray);
+    assert.ok(band.embeddedMembers.isMongooseArray);
     assert.ok(!band.embeddedMembers[0].member.name);
+    // assert.ok(!band.embeddedMembers[0].$populated('member'));
   });
 
   it('should allow dashes in the path name (gh-10677)', async function() {