diff --git a/worker/pkg/select-query-builder/querybuilder.go b/worker/pkg/select-query-builder/querybuilder.go
index a9a3c1257f..4512583a83 100644
--- a/worker/pkg/select-query-builder/querybuilder.go
+++ b/worker/pkg/select-query-builder/querybuilder.go
@@ -379,14 +379,20 @@ func qualifyMysqlWhereColumnNames(sql string, schema *string, table string) (str
 		err = sqlparser.Walk(func(node sqlparser.SQLNode) (kontinue bool, err error) {
 			switch node := node.(type) { //nolint:gocritic
 			case *sqlparser.ComparisonExpr:
-				if col, ok := node.Left.(*sqlparser.ColName); ok {
-					s := ""
-					if schema != nil && *schema != "" {
-						s = *schema
+				qualifyColumn := func(expr sqlparser.Expr) {
+					if col, ok := expr.(*sqlparser.ColName); ok {
+						if col.Qualifier.Name.String() == "" {
+							s := ""
+							if schema != nil && *schema != "" {
+								s = *schema
+							}
+							col.Qualifier.Qualifier = sqlparser.NewTableIdent(s)
+							col.Qualifier.Name = sqlparser.NewTableIdent(table)
+						}
 					}
-					col.Qualifier.Qualifier = sqlparser.NewTableIdent(s)
-					col.Qualifier.Name = sqlparser.NewTableIdent(table)
 				}
+				qualifyColumn(node.Left)
+				qualifyColumn(node.Right)
 				return false, nil
 			}
 			return true, nil
diff --git a/worker/pkg/select-query-builder/querybuilder_test.go b/worker/pkg/select-query-builder/querybuilder_test.go
new file mode 100644
index 0000000000..68fd3f78e3
--- /dev/null
+++ b/worker/pkg/select-query-builder/querybuilder_test.go
@@ -0,0 +1,71 @@
+package selectquerybuilder
+
+import (
+	"testing"
+
+	sqlmanager_shared "github.com/nucleuscloud/neosync/backend/pkg/sqlmanager/shared"
+	"github.com/nucleuscloud/neosync/internal/runconfigs"
+	"github.com/stretchr/testify/assert"
+)
+
+func Test_BuildQuery_MySQLColumnQualification(t *testing.T) {
+	t.Run("mysql column on left", func(t *testing.T) {
+		assert.Equal(t,
+			"SELECT `orders`.`order_id`, `orders`.`user_id` FROM `public`.`orders` AS `orders` INNER JOIN `public`.`users` AS `t_09a0eed1cbbe07ca` ON (`t_09a0eed1cbbe07ca`.`user_id` = `orders`.`user_id`) WHERE t_09a0eed1cbbe07ca.user_id < 100 ORDER BY `orders`.`order_id` ASC",
+			buildOrdersUsersSubsettingQuery(t, "user_id < 100", sqlmanager_shared.MysqlDriver),
+		)
+	})
+
+	t.Run("mysql column on right", func(t *testing.T) {
+		assert.Equal(t,
+			"SELECT `orders`.`order_id`, `orders`.`user_id` FROM `public`.`orders` AS `orders` INNER JOIN `public`.`users` AS `t_09a0eed1cbbe07ca` ON (`t_09a0eed1cbbe07ca`.`user_id` = `orders`.`user_id`) WHERE 100 > t_09a0eed1cbbe07ca.user_id ORDER BY `orders`.`order_id` ASC",
+			buildOrdersUsersSubsettingQuery(t, "100 > user_id", sqlmanager_shared.MysqlDriver),
+		)
+	})
+}
+
+func buildOrdersUsersSubsettingQuery(t *testing.T, whereClause, driver string) string {
+	t.Helper()
+
+	runConfigs, err := runconfigs.BuildRunConfigs(
+		map[string][]*sqlmanager_shared.ForeignConstraint{
+			"public.orders": {{
+				Columns:     []string{"user_id"},
+				NotNullable: []bool{true},
+				ForeignKey: &sqlmanager_shared.ForeignKey{
+					Table:   "public.users",
+					Columns: []string{"user_id"},
+				},
+			}},
+		},
+		map[string]string{"public.users": whereClause},
+		map[string][]string{
+			"public.orders": {"order_id"},
+			"public.users":  {"user_id"},
+		},
+		map[string][]string{
+			"public.orders": {"order_id", "user_id"},
+			"public.users":  {"user_id"},
+		},
+		map[string][][]string{},
+		map[string][][]string{},
+	)
+	assert.NoError(t, err)
+
+	var ordersConfig *runconfigs.RunConfig
+
+	for _, rc := range runConfigs {
+		if rc.Table() == "public.orders" {
+			ordersConfig = rc
+
+			break
+		}
+	}
+
+	assert.NotNil(t, ordersConfig)
+
+	query, _, _, _, err := NewSelectQueryBuilder("public", driver, true, 0).BuildQuery(ordersConfig)
+	assert.NoError(t, err)
+
+	return query
+}