diff --git a/flow/connectors/bigquery/merge_stmt_generator.go b/flow/connectors/bigquery/merge_stmt_generator.go
index eb8ebb6177..cca68cdda7 100644
--- a/flow/connectors/bigquery/merge_stmt_generator.go
+++ b/flow/connectors/bigquery/merge_stmt_generator.go
@@ -2,6 +2,7 @@ package connbigquery
 
 import (
 	"fmt"
+	"slices"
 	"strings"
 
 	"cloud.google.com/go/bigquery"
@@ -100,6 +101,22 @@ func (m *mergeStmtGenerator) generateFlattenedCTE() string {
 		m.syncBatchID, m.dstTableName)
 }
 
+func (m *mergeStmtGenerator) transformedPkeyStrings() []string {
+	pkeys := make([]string, 0, len(m.normalizedTableSchema.PrimaryKeyColumns))
+	for _, col := range m.normalizedTableSchema.Columns {
+		if slices.Contains(m.normalizedTableSchema.PrimaryKeyColumns, col.Name) {
+			pkeyCol := col.Name
+			switch qvalue.QValueKind(col.Type) {
+			case qvalue.QValueKindJSON:
+				pkeys = append(pkeys, fmt.Sprintf("TO_JSON_STRING(%s)", m.shortColumn[pkeyCol]))
+			default:
+				pkeys = append(pkeys, m.shortColumn[pkeyCol])
+			}
+		}
+	}
+	return pkeys
+}
+
 // generateDeDupedCTE generates a de-duped CTE.
 func (m *mergeStmtGenerator) generateDeDupedCTE() string {
 	const cte = `_dd AS (
@@ -111,11 +128,7 @@ func (m *mergeStmtGenerator) generateDeDupedCTE() string {
 			WHERE _peerdb_rank=1
 	) SELECT * FROM _dd`
 
-	shortPkeys := make([]string, 0, len(m.normalizedTableSchema.PrimaryKeyColumns))
-	for _, pkeyCol := range m.normalizedTableSchema.PrimaryKeyColumns {
-		shortPkeys = append(shortPkeys, m.shortColumn[pkeyCol])
-	}
-
+	shortPkeys := m.transformedPkeyStrings()
 	pkeyColsStr := fmt.Sprintf("(CONCAT(%s))", strings.Join(shortPkeys,
 		", '_peerdb_concat_', "))
 	return fmt.Sprintf(cte, pkeyColsStr)
diff --git a/flow/e2e/bigquery/peer_flow_bq_test.go b/flow/e2e/bigquery/peer_flow_bq_test.go
index 9d0b8f6a57..74a1949ff7 100644
--- a/flow/e2e/bigquery/peer_flow_bq_test.go
+++ b/flow/e2e/bigquery/peer_flow_bq_test.go
@@ -1514,3 +1514,56 @@ func (s PeerFlowE2ETestSuiteBQ) Test_Soft_Delete_Insert_After_Delete() {
 	require.NoError(s.t, err)
 	require.Equal(s.t, int64(0), numNewRows)
 }
+
+func (s PeerFlowE2ETestSuiteBQ) Test_JSON_PKey_BQ() {
+	env := e2e.NewTemporalTestWorkflowEnvironment(s.t)
+
+	srcTableName := s.attachSchemaSuffix("test_json_pkey_bq")
+	dstTableName := "test_json_pkey_bq"
+
+	_, err := s.Conn().Exec(context.Background(), fmt.Sprintf(`
+	CREATE TABLE IF NOT EXISTS %s (
+		id SERIAL NOT NULL,
+		j JSON NOT NULL,
+		key TEXT NOT NULL,
+		value TEXT NOT NULL
+	);
+	`, srcTableName))
+	require.NoError(s.t, err)
+
+	_, err = s.Conn().Exec(context.Background(), fmt.Sprintf(`
+		ALTER TABLE %s REPLICA IDENTITY FULL
+		`, srcTableName))
+	require.NoError(s.t, err)
+
+	connectionGen := e2e.FlowConnectionGenerationConfig{
+		FlowJobName:      s.attachSuffix("test_json_pkey_flow"),
+		TableNameMapping: map[string]string{srcTableName: dstTableName},
+		Destination:      s.bqHelper.Peer,
+		CdcStagingPath:   "",
+	}
+
+	flowConnConfig := connectionGen.GenerateFlowConnectionConfigs()
+	flowConnConfig.MaxBatchSize = 100
+
+	go func() {
+		e2e.SetupCDCFlowStatusQuery(s.t, env, connectionGen)
+		// insert 10 rows into the source table
+		for i := range 10 {
+			testKey := fmt.Sprintf("test_key_%d", i)
+			testValue := fmt.Sprintf("test_value_%d", i)
+			testJson := `'{"name":"jack", "age":12, "spouse":null}'::json`
+			_, err = s.Conn().Exec(context.Background(), fmt.Sprintf(`
+			INSERT INTO %s(key, value, j) VALUES ($1, $2, %s)
+		`, srcTableName, testJson), testKey, testValue)
+			e2e.EnvNoError(s.t, env, err)
+		}
+		s.t.Log("Inserted 10 rows into the source table")
+
+		e2e.EnvWaitForEqualTables(env, s, "normalize inserts", dstTableName, "id,key,value,j")
+		env.CancelWorkflow()
+	}()
+
+	env.ExecuteWorkflow(peerflow.CDCFlowWorkflow, flowConnConfig, nil)
+	e2e.RequireEnvCanceled(s.t, env)
+}