diff --git a/go/vt/sqlparser/ast_funcs.go b/go/vt/sqlparser/ast_funcs.go
index 201a0b8315c..af57e02ee88 100644
--- a/go/vt/sqlparser/ast_funcs.go
+++ b/go/vt/sqlparser/ast_funcs.go
@@ -2145,6 +2145,18 @@ func RemoveKeyspace(in SQLNode) {
 	}, in)
 }
 
+// RemoveKeyspaceInTables removes the database qualifier for all table names in the AST
+func RemoveKeyspaceInTables(in SQLNode) {
+	Rewrite(in, nil, func(cursor *Cursor) bool {
+		if tbl, ok := cursor.Node().(TableName); ok && !tbl.Qualifier.IsEmpty() {
+			tbl.Qualifier = NewIdentifierCS("")
+			cursor.Replace(tbl)
+		}
+
+		return true
+	})
+}
+
 func convertStringToInt(integer string) int {
 	val, _ := strconv.Atoi(integer)
 	return val
diff --git a/go/vt/vtgate/planbuilder/operators/merging.go b/go/vt/vtgate/planbuilder/operators/merging.go
index ef8da1ef280..6055eb4354d 100644
--- a/go/vt/vtgate/planbuilder/operators/merging.go
+++ b/go/vt/vtgate/planbuilder/operators/merging.go
@@ -274,6 +274,8 @@ func (s *subQueryMerger) markPredicateInOuterRouting(outer *ShardedRouting, inne
 
 func (s *subQueryMerger) mergeTables(outer, inner *ShardedRouting, op1, op2 *Route) (*Route, error) {
 	s.subq.ExtractedSubquery.Merged = true
+	// we need to make sure that table qualifiers are removed before sending the query to MySQL
+	sqlparser.RemoveKeyspaceInTables(s.subq.ExtractedSubquery)
 
 	routing, err := s.markPredicateInOuterRouting(outer, inner)
 	if err != nil {
diff --git a/go/vt/vtgate/planbuilder/testdata/filter_cases.json b/go/vt/vtgate/planbuilder/testdata/filter_cases.json
index c596875f2df..e4f92c6b226 100644
--- a/go/vt/vtgate/planbuilder/testdata/filter_cases.json
+++ b/go/vt/vtgate/planbuilder/testdata/filter_cases.json
@@ -846,6 +846,44 @@
       ]
     }
   },
+  {
+    "comment": "Merging subqueries should remove keyspace from query",
+    "query": "select u.id from user.user as u where not exists (select 1 from user.user_extra as ue where u.id = ue.user_id)",
+    "v3-plan": {
+      "QueryType": "SELECT",
+      "Original": "select u.id from user.user as u where not exists (select 1 from user.user_extra as ue where u.id = ue.user_id)",
+      "Instructions": {
+        "OperatorType": "Route",
+        "Variant": "Scatter",
+        "Keyspace": {
+          "Name": "user",
+          "Sharded": true
+        },
+        "FieldQuery": "select u.id from `user` as u where 1 != 1",
+        "Query": "select u.id from `user` as u where not exists (select 1 from user_extra as ue where u.id = ue.user_id limit 1)",
+        "Table": "`user`"
+      }
+    },
+    "gen4-plan": {
+      "QueryType": "SELECT",
+      "Original": "select u.id from user.user as u where not exists (select 1 from user.user_extra as ue where u.id = ue.user_id)",
+      "Instructions": {
+        "OperatorType": "Route",
+        "Variant": "Scatter",
+        "Keyspace": {
+          "Name": "user",
+          "Sharded": true
+        },
+        "FieldQuery": "select u.id from `user` as u where 1 != 1",
+        "Query": "select u.id from `user` as u where not exists (select 1 from user_extra as ue where u.id = ue.user_id limit 1)",
+        "Table": "`user`"
+      },
+      "TablesUsed": [
+        "user.user",
+        "user.user_extra"
+      ]
+    }
+  },
   {
     "comment": "Composite IN: tuple inside tuple",
     "query": "select id from user where ((col1, name), col2) in ((('aa', 'bb'), 'cc'), (('dd', 'ee'), 'ff'))",