diff --git a/frappe/model/db_query.py b/frappe/model/db_query.py
index a43d0ad2dc..87e3d83e9c 100644
--- a/frappe/model/db_query.py
+++ b/frappe/model/db_query.py
@@ -613,7 +613,10 @@ class DatabaseQuery:
 
 		elif f.operator.lower() in ("in", "not in"):
 			# if values contain '' or falsy values then only coalesce column
-			can_be_null = not f.value or any(v is None or v == "" for v in f.value)
+			# for `in` query this is only required if values contain '' or values are empty.
+			# for `not in` queries we can't be sure as column values might contain null.
+			if f.operator.lower() == "in":
+				can_be_null = not f.value or any(v is None or v == "" for v in f.value)
 
 			values = f.value or ""
 			if isinstance(values, str):
diff --git a/frappe/tests/test_db_query.py b/frappe/tests/test_db_query.py
index 881b90f399..9e61c5d3ec 100644
--- a/frappe/tests/test_db_query.py
+++ b/frappe/tests/test_db_query.py
@@ -749,6 +749,10 @@ class TestReportview(FrappeTestCase):
 		self.assertNotIn("ifnull", frappe.get_all("User", {"name": ("in", ["a", "b"])}, run=0))
 		self.assertIn("ifnull", frappe.get_all("User", {"name": ("in", ["a", None])}, run=0))
 		self.assertIn("ifnull", frappe.get_all("User", {"name": ("in", ["a", ""])}, run=0))
+		self.assertIn("ifnull", frappe.get_all("User", {"name": ("in", [])}, run=0))
+		self.assertIn("ifnull", frappe.get_all("User", {"name": ("not in", ["a"])}, run=0))
+		self.assertIn("ifnull", frappe.get_all("User", {"name": ("not in", [])}, run=0))
+		self.assertIn("ifnull", frappe.get_all("User", {"name": ("not in", [""])}, run=0))
 
 
 def add_child_table_to_blog_post():