diff --git a/django/db/models/sql/query.py b/django/db/models/sql/query.py
index f332d83946..f0865f5f78 100644
--- a/django/db/models/sql/query.py
+++ b/django/db/models/sql/query.py
@@ -1249,12 +1249,11 @@ class Query(BaseExpression):
 
     @property
     def _subquery_fields_len(self):
-        if self.has_select_fields:
-            return sum(
-                len(self.model._meta.pk_fields) if field == "pk" else 1
-                for field in self.selected
-            )
-        return len(self.model._meta.pk_fields)
+        if not self.has_select_fields or not self.select:
+            return len(self.model._meta.pk_fields)
+        return len(self.select) + sum(
+            len(expr.targets) - 1 for expr in self.select if isinstance(expr, ColPairs)
+        )
 
     def resolve_expression(self, query, *args, **kwargs):
         clone = self.clone()
diff --git a/tests/composite_pk/test_filter.py b/tests/composite_pk/test_filter.py
index d7ecfbec11..c4b393d6ea 100644
--- a/tests/composite_pk/test_filter.py
+++ b/tests/composite_pk/test_filter.py
@@ -460,6 +460,11 @@ class CompositePKFilterTests(TestCase):
         queryset = User.objects.filter(comments__in=subquery)
         self.assertSequenceEqual(queryset, (self.user_2,))
 
+    def test_filter_comments_by_users_subquery(self):
+        subquery = Comment.objects.filter(id=3).values("user")
+        queryset = Comment.objects.filter(user__in=subquery)
+        self.assertSequenceEqual(queryset, (self.comment_3,))
+
     def test_cannot_cast_pk(self):
         msg = "Cast expression does not support composite primary keys."
         with self.assertRaisesMessage(ValueError, msg):