diff --git a/docs/changelog.rst b/docs/changelog.rst
index 887a67773..95aeb3ce0 100644
--- a/docs/changelog.rst
+++ b/docs/changelog.rst
@@ -22,7 +22,7 @@ Development
 - Add support for collation/hint/comment to delete/update and aggregate #2842
 - BREAKING CHANGE: Remove LongField as it's equivalent to IntField since we drop support to Python2 long time ago (User should simply switch to IntField) #2309
 - BugFix - Calling .clear on a ListField wasn't being marked as changed (and flushed to db upon .save()) #2858
-
+- BugFix - Take `where()` into account when using `.modify()`, as in MyDocument.objects().where("this[field] >= this[otherfield]").modify(field='new') #2044
 
 Changes in 0.29.0
 =================
diff --git a/mongoengine/queryset/base.py b/mongoengine/queryset/base.py
index f04ef06c5..2db97ddb7 100644
--- a/mongoengine/queryset/base.py
+++ b/mongoengine/queryset/base.py
@@ -727,6 +727,11 @@ def modify(
 
         queryset = self.clone()
         query = queryset._query
+
+        if self._where_clause:
+            where_clause = self._sub_js_fields(self._where_clause)
+            query["$where"] = where_clause
+
         if not remove:
             update = transform.update(queryset._document, **update)
         sort = queryset._ordering
diff --git a/tests/queryset/test_queryset.py b/tests/queryset/test_queryset.py
index 0b8773c2b..8386249f2 100644
--- a/tests/queryset/test_queryset.py
+++ b/tests/queryset/test_queryset.py
@@ -28,6 +28,7 @@
 from mongoengine.queryset.base import BaseQuerySet
 from tests.utils import (
     db_ops_tracker,
+    get_as_pymongo,
     requires_mongodb_gte_42,
     requires_mongodb_gte_44,
     requires_mongodb_lt_42,
@@ -4456,7 +4457,7 @@ class Comment(Document):
         ]
         assert ([("_cls", 1), ("message", 1)], False, False) in info
 
-    def test_where(self):
+    def test_where_query(self):
         """Ensure that where clauses work."""
 
         class IntPair(Document):
@@ -4499,6 +4500,60 @@ class IntPair(Document):
         with pytest.raises(TypeError):
             list(IntPair.objects.where(fielda__gte=3))
 
+    def test_where_query_field_name_subs(self):
+        class DomainObj(Document):
+            field_1 = StringField(db_field="field_2")
+
+        DomainObj.drop_collection()
+
+        DomainObj(field_1="test").save()
+
+        obj = DomainObj.objects.where("this[~field_1] == 'NOTMATCHING'")
+        assert not list(obj)
+
+        obj = DomainObj.objects.where("this[~field_1] == 'test'")
+        assert list(obj)
+
+    def test_where_modify(self):
+        class DomainObj(Document):
+            field = StringField()
+
+        DomainObj.drop_collection()
+
+        DomainObj(field="test").save()
+
+        obj = DomainObj.objects.where("this[~field] == 'NOTMATCHING'")
+        assert not list(obj)
+
+        obj = DomainObj.objects.where("this[~field] == 'test'")
+        assert list(obj)
+
+        qs = DomainObj.objects.where("this[~field] == 'NOTMATCHING'").modify(
+            field="new"
+        )
+        assert not qs
+
+        qs = DomainObj.objects.where("this[~field] == 'test'").modify(field="new")
+        assert qs
+
+    def test_where_modify_field_name_subs(self):
+        class DomainObj(Document):
+            field_1 = StringField(db_field="field_2")
+
+        DomainObj.drop_collection()
+
+        DomainObj(field_1="test").save()
+
+        obj = DomainObj.objects.where("this[~field_1] == 'NOTMATCHING'").modify(
+            field_1="new"
+        )
+        assert not obj
+
+        obj = DomainObj.objects.where("this[~field_1] == 'test'").modify(field_1="new")
+        assert obj
+
+        assert get_as_pymongo(obj) == {"_id": obj.id, "field_2": "new"}
+
     def test_scalar(self):
         class Organization(Document):
             name = StringField()