diff --git a/flow/connectors/mysql/cdc.go b/flow/connectors/mysql/cdc.go
index 77a4cbfc6..6afd11b8c 100644
--- a/flow/connectors/mysql/cdc.go
+++ b/flow/connectors/mysql/cdc.go
@@ -1,6 +1,7 @@
 package connmysql
 
 import (
+	"bytes"
 	"cmp"
 	"context"
 	"crypto/tls"
@@ -44,6 +45,10 @@ func (c *MySqlConnector) binlogStalenessThreshold() time.Duration {
 	return binlogStalenessMultiplier * c.binlogHeartbeatPeriod
 }
 
+func trimQueryEventSQL(query []byte) string {
+	return shared.UnsafeFastReadOnlyBytesToString(bytes.TrimRight(query, "\x00"))
+}
+
 func (c *MySqlConnector) GetTableSchema(
 	ctx context.Context,
 	env map[string]string,
@@ -569,7 +574,7 @@ func (c *MySqlConnector) PullRecords(
 			if mysqlParser == nil {
 				mysqlParser = parser.New()
 			}
-			stmts, warns, err := mysqlParser.ParseSQL(shared.UnsafeFastReadOnlyBytesToString(ev.Query))
+			stmts, warns, err := mysqlParser.ParseSQL(trimQueryEventSQL(ev.Query))
 			if err != nil {
 				c.logger.Warn("failed to parse QueryEvent", slog.String("query", string(ev.Query)), slog.Any("error", err))
 				break
@@ -577,12 +582,31 @@ func (c *MySqlConnector) PullRecords(
 			if len(warns) > 0 {
 				c.logger.Warn("processing QueryEvent with logged warnings", slog.Any("warns", warns))
 			}
+			advanceTransactionCheckpoint := func() {
+				if gset != nil {
+					gset = ev.GSet
+					updatedOffset = gset.String()
+					req.RecordStream.UpdateLatestCheckpointText(updatedOffset)
+				} else if event.Header.LogPos > pos.Pos {
+					pos.Pos = event.Header.LogPos
+					updatedOffset = posToOffsetText(pos)
+					req.RecordStream.UpdateLatestCheckpointText(updatedOffset)
+				}
+				inTx = false
+			}
 			for _, stmt := range stmts {
-				if alterTableStmt, ok := stmt.(*ast.AlterTableStmt); ok {
+				switch stmt := stmt.(type) {
+				case *ast.AlterTableStmt:
 					if err := c.processAlterTableQuery(
-						ctx, catalogPool, req, alterTableStmt, string(ev.Schema), binlogRowMetadataSupported, req.InternalVersion); err != nil {
+						ctx, catalogPool, req, stmt, string(ev.Schema), binlogRowMetadataSupported, req.InternalVersion); err != nil {
 						return fmt.Errorf("failed to process ALTER TABLE query: %w", err)
 					}
+				case *ast.CommitStmt:
+					advanceTransactionCheckpoint()
+				case *ast.RollbackStmt:
+					if stmt.SavepointName == "" {
+						advanceTransactionCheckpoint()
+					}
 				}
 			}
 		case *replication.RowsEvent:
diff --git a/flow/connectors/mysql/cdc_test.go b/flow/connectors/mysql/cdc_test.go
index 3ed471271..7daa2e76b 100644
--- a/flow/connectors/mysql/cdc_test.go
+++ b/flow/connectors/mysql/cdc_test.go
@@ -5,6 +5,8 @@ import (
 	"fmt"
 	"testing"
 
+	"github.com/pingcap/tidb/pkg/parser"
+	"github.com/pingcap/tidb/pkg/parser/ast"
 	"github.com/stretchr/testify/require"
 
 	"github.com/PeerDB-io/peerdb/flow/generated/protos"
@@ -50,6 +52,43 @@ func createTestDB(t *testing.T, ctx context.Context, c *MySqlConnector, dbName s
 	})
 }
 
+func TestTrimQueryEventSQLParsesTrailingNull(t *testing.T) {
+	for _, tc := range []struct {
+		name   string
+		query  []byte
+		assert func(*testing.T, ast.StmtNode)
+	}{
+		{
+			name:  "alter table",
+			query: []byte("ALTER TABLE t ADD COLUMN c INT\x00"),
+			assert: func(t *testing.T, stmt ast.StmtNode) {
+				t.Helper()
+				require.IsType(t, &ast.AlterTableStmt{}, stmt)
+			},
+		},
+		{
+			name:  "commit",
+			query: []byte("COMMIT\x00"),
+			assert: func(t *testing.T, stmt ast.StmtNode) {
+				t.Helper()
+				require.IsType(t, &ast.CommitStmt{}, stmt)
+			},
+		},
+	} {
+		t.Run(tc.name, func(t *testing.T) {
+			mysqlParser := parser.New()
+			_, _, err := mysqlParser.ParseSQL(string(tc.query))
+			require.Error(t, err)
+
+			stmts, warns, err := mysqlParser.ParseSQL(trimQueryEventSQL(tc.query))
+			require.NoError(t, err)
+			require.Empty(t, warns)
+			require.Len(t, stmts, 1)
+			tc.assert(t, stmts[0])
+		})
+	}
+}
+
 func TestGetTableSchemaCaseSensitiveIdentifiers(t *testing.T) {
 	t.Parallel()
 	ctx := t.Context()
diff --git a/flow/e2e/clickhouse_mysql_test.go b/flow/e2e/clickhouse_mysql_test.go
index 727d50d29..25bbac0b9 100644
--- a/flow/e2e/clickhouse_mysql_test.go
+++ b/flow/e2e/clickhouse_mysql_test.go
@@ -230,6 +230,48 @@ func (s ClickHouseSuite) Test_MySQL_Blobs() {
 	RequireEnvCanceled(s.t, env)
 }
 
+func (s ClickHouseSuite) Test_MySQL_NonTransactionalEngineCDC() {
+	if _, ok := s.source.(*MySqlSource); !ok || internal.MySQLTestVersionIsMaria() {
+		s.t.Skip("only applies to mysql")
+	}
+
+	srcTableName := "test_non_transactional_engine"
+	srcFullName := s.attachSchemaSuffix(srcTableName)
+	dstTableName := "test_non_transactional_engine_dst"
+
+	require.NoError(s.t, s.source.Exec(s.t.Context(), fmt.Sprintf(`
+		CREATE TABLE IF NOT EXISTS %s (
+			id INT PRIMARY KEY,
+			val TEXT NOT NULL
+		) ENGINE=MyISAM
+	`, srcFullName)))
+
+	require.NoError(s.t, s.source.Exec(s.t.Context(), fmt.Sprintf(
+		`INSERT INTO %s (id,val) VALUES (1,'snapshot')`, srcFullName)))
+
+	connectionGen := FlowConnectionGenerationConfig{
+		FlowJobName:      s.attachSuffix(srcTableName),
+		TableNameMapping: map[string]string{srcFullName: dstTableName},
+		Destination:      s.Peer().Name,
+	}
+	flowConnConfig := connectionGen.GenerateFlowConnectionConfigs(s)
+	flowConnConfig.DoInitialSnapshot = true
+
+	tc := NewTemporalClient(s.t)
+	env := ExecutePeerflow(s.t, tc, flowConnConfig)
+	SetupCDCFlowStatusQuery(s.t, env, flowConnConfig)
+
+	EnvWaitForEqualTablesWithNames(env, s, "snapshot", srcTableName, dstTableName, "id,val")
+
+	require.NoError(s.t, s.source.Exec(s.t.Context(), fmt.Sprintf(
+		`INSERT INTO %s (id,val) VALUES (2,'cdc')`, srcFullName)))
+
+	EnvWaitForEqualTablesWithNames(env, s, "cdc", srcTableName, dstTableName, "id,val")
+
+	env.Cancel(s.t.Context())
+	RequireEnvCanceled(s.t, env)
+}
+
 // Test_MySQL_Binary_Trailing_Zeros reproduces trailing-0x00 truncation of fixed-length
 // BINARY(N) columns over CDC.
 //