diff --git a/go/mysql/flavor.go b/go/mysql/flavor.go
index 26adb83f145..72cd460d7da 100644
--- a/go/mysql/flavor.go
+++ b/go/mysql/flavor.go
@@ -76,6 +76,9 @@ type flavor interface {
 	// stopIOThreadCommand returns the command to stop the replica's io thread only.
 	stopIOThreadCommand() string
 
+	// startSQLThreadCommand returns the command to start the replica's sql thread only.
+	startSQLThreadCommand() string
+
 	// sendBinlogDumpCommand sends the packet required to start
 	// dumping binlogs from the specified location.
 	sendBinlogDumpCommand(c *Conn, serverID uint32, startPos Position) error
@@ -224,6 +227,11 @@ func (c *Conn) StopIOThreadCommand() string {
 	return c.flavor.stopIOThreadCommand()
 }
 
+// StartSQLThreadCommand returns the command to start the replica's SQL thread.
+func (c *Conn) StartSQLThreadCommand() string {
+	return c.flavor.startSQLThreadCommand()
+}
+
 // SendBinlogDumpCommand sends the flavor-specific version of
 // the COM_BINLOG_DUMP command to start dumping raw binlog
 // events over a server connection, starting at a given GTID.
diff --git a/go/mysql/flavor_filepos.go b/go/mysql/flavor_filepos.go
index fcae889c7f1..d5d7fd59c0e 100644
--- a/go/mysql/flavor_filepos.go
+++ b/go/mysql/flavor_filepos.go
@@ -78,6 +78,10 @@ func (flv *filePosFlavor) stopIOThreadCommand() string {
 	return "unsupported"
 }
 
+func (flv *filePosFlavor) startSQLThreadCommand() string {
+	return "unsupported"
+}
+
 // sendBinlogDumpCommand is part of the Flavor interface.
 func (flv *filePosFlavor) sendBinlogDumpCommand(c *Conn, serverID uint32, startPos Position) error {
 	rpos, ok := startPos.GTIDSet.(filePosGTID)
diff --git a/go/mysql/flavor_mariadb.go b/go/mysql/flavor_mariadb.go
index cf53e6e6521..abca919f6d8 100644
--- a/go/mysql/flavor_mariadb.go
+++ b/go/mysql/flavor_mariadb.go
@@ -77,6 +77,10 @@ func (mariadbFlavor) stopIOThreadCommand() string {
 	return "STOP SLAVE IO_THREAD"
 }
 
+func (mariadbFlavor) startSQLThreadCommand() string {
+	return "START SLAVE SQL_THREAD"
+}
+
 // sendBinlogDumpCommand is part of the Flavor interface.
 func (mariadbFlavor) sendBinlogDumpCommand(c *Conn, serverID uint32, startPos Position) error {
 	// Tell the server that we understand GTIDs by setting
diff --git a/go/mysql/flavor_mysql.go b/go/mysql/flavor_mysql.go
index 0e23f889cc8..fcc25b14380 100644
--- a/go/mysql/flavor_mysql.go
+++ b/go/mysql/flavor_mysql.go
@@ -80,6 +80,10 @@ func (mysqlFlavor) stopIOThreadCommand() string {
 	return "STOP SLAVE IO_THREAD"
 }
 
+func (mysqlFlavor) startSQLThreadCommand() string {
+	return "START SLAVE SQL_THREAD"
+}
+
 // sendBinlogDumpCommand is part of the Flavor interface.
 func (mysqlFlavor) sendBinlogDumpCommand(c *Conn, serverID uint32, startPos Position) error {
 	gtidSet, ok := startPos.GTIDSet.(Mysql56GTIDSet)
diff --git a/go/mysql/flavor_mysqlgr.go b/go/mysql/flavor_mysqlgr.go
index 196c632fb7c..4e8ed7c7dd3 100644
--- a/go/mysql/flavor_mysqlgr.go
+++ b/go/mysql/flavor_mysqlgr.go
@@ -73,6 +73,11 @@ func (mysqlGRFlavor) stopIOThreadCommand() string {
 	return ""
 }
 
+// startSQLThreadCommand is disabled in mysqlGRFlavor
+func (mysqlGRFlavor) startSQLThreadCommand() string {
+	return ""
+}
+
 // resetReplicationCommands is disabled in mysqlGRFlavor
 func (mysqlGRFlavor) resetReplicationCommands(c *Conn) []string {
 	return []string{}
diff --git a/go/test/endtoend/cluster/cluster_process.go b/go/test/endtoend/cluster/cluster_process.go
index 2dbebccfc5d..d14104a1ad0 100644
--- a/go/test/endtoend/cluster/cluster_process.go
+++ b/go/test/endtoend/cluster/cluster_process.go
@@ -26,6 +26,7 @@ import (
 	"os/exec"
 	"os/signal"
 	"path"
+	"regexp"
 	"strconv"
 	"sync"
 	"syscall"
@@ -72,6 +73,10 @@ type LocalProcessCluster struct {
 	VtgateGrpcPort  int
 	VtctldHTTPPort  int
 
+	// major version numbers
+	VtTabletMajorVersion int
+	VtctlMajorVersion    int
+
 	// standalone executable
 	VtctlclientProcess VtctlClientProcess
 	VtctlProcess       VtctlProcess
@@ -212,6 +217,7 @@ func (cluster *LocalProcessCluster) StartTopo() (err error) {
 			log.Error(err)
 			return
 		}
+		cluster.VtctlProcess.LogDir = cluster.TmpDirectory
 	}
 
 	cluster.VtctldProcess = *VtctldProcessInstance(cluster.GetAndReservePort(), cluster.GetAndReservePort(),
@@ -627,10 +633,42 @@ func NewCluster(cell string, hostname string) *LocalProcessCluster {
 	_ = os.Setenv("VTDATAROOT", cluster.CurrentVTDATAROOT)
 	log.Infof("Created cluster on %s. ReusingVTDATAROOT=%v", cluster.CurrentVTDATAROOT, cluster.ReusingVTDATAROOT)
 
+	err := cluster.populateVersionInfo()
+	if err != nil {
+		log.Errorf("Error populating version information - %v", err)
+	}
+
 	rand.Seed(time.Now().UTC().UnixNano())
 	return cluster
 }
 
+// populateVersionInfo is used to populate the version information for the binaries used to setup the cluster.
+func (cluster *LocalProcessCluster) populateVersionInfo() error {
+	var err error
+	cluster.VtTabletMajorVersion, err = getMajorVersion("vttablet")
+	if err != nil {
+		return err
+	}
+	cluster.VtctlMajorVersion, err = getMajorVersion("vtctl")
+	return err
+}
+
+func getMajorVersion(binaryName string) (int, error) {
+	version, err := exec.Command(binaryName, "--version").Output()
+	if err != nil {
+		return 0, err
+	}
+	versionRegex := regexp.MustCompile(`Version: ([0-9]+)\.([0-9]+)\.([0-9]+)`)
+	v := versionRegex.FindStringSubmatch(string(version))
+	if len(v) != 4 {
+		return 0, fmt.Errorf("could not parse server version from: %s", version)
+	}
+	if err != nil {
+		return 0, fmt.Errorf("could not parse server version from: %s", version)
+	}
+	return strconv.Atoi(v[1])
+}
+
 // RestartVtgate starts vtgate with updated configs
 func (cluster *LocalProcessCluster) RestartVtgate() (err error) {
 	err = cluster.VtgateProcess.TearDown()
diff --git a/go/test/endtoend/cluster/vtctl_process.go b/go/test/endtoend/cluster/vtctl_process.go
index b27cdea9911..c47219eb98e 100644
--- a/go/test/endtoend/cluster/vtctl_process.go
+++ b/go/test/endtoend/cluster/vtctl_process.go
@@ -29,6 +29,7 @@ import (
 type VtctlProcess struct {
 	Name               string
 	Binary             string
+	LogDir             string
 	TopoImplementation string
 	TopoGlobalAddress  string
 	TopoGlobalRoot     string
@@ -68,6 +69,7 @@ func (vtctl *VtctlProcess) CreateKeyspace(keyspace string) (err error) {
 // ExecuteCommandWithOutput executes any vtctlclient command and returns output
 func (vtctl *VtctlProcess) ExecuteCommandWithOutput(args ...string) (result string, err error) {
 	args = append([]string{
+		"-log_dir", vtctl.LogDir,
 		"-enable_queries",
 		"-topo_implementation", vtctl.TopoImplementation,
 		"-topo_global_server_address", vtctl.TopoGlobalAddress,
diff --git a/go/test/endtoend/reparent/newfeaturetest/reparent_test.go b/go/test/endtoend/reparent/newfeaturetest/reparent_test.go
index ee68bbb167f..393da0f6e70 100644
--- a/go/test/endtoend/reparent/newfeaturetest/reparent_test.go
+++ b/go/test/endtoend/reparent/newfeaturetest/reparent_test.go
@@ -218,9 +218,10 @@ func TestPullFromRdonly(t *testing.T) {
 	require.NoError(t, err)
 }
 
-// TestTwoReplicasNoReplicationStatus checks that ERS is able to fix
-// two replicas which do not have any replication status
-func TestTwoReplicasNoReplicationStatus(t *testing.T) {
+// TestNoReplicationStatusAndReplicationStopped checks that ERS is able to fix
+// replicas which do not have any replication status and also succeeds if the replication
+// is stopped on the primary elect.
+func TestNoReplicationStatusAndReplicationStopped(t *testing.T) {
 	defer cluster.PanicHandler(t)
 	clusterInstance := utils.SetupReparentCluster(t)
 	defer utils.TeardownCluster(clusterInstance)
@@ -229,11 +230,22 @@ func TestTwoReplicasNoReplicationStatus(t *testing.T) {
 
 	err := clusterInstance.VtctlclientProcess.ExecuteCommand("ExecuteFetchAsDba", tablets[1].Alias, `STOP SLAVE; RESET SLAVE ALL`)
 	require.NoError(t, err)
-	err = clusterInstance.VtctlclientProcess.ExecuteCommand("ExecuteFetchAsDba", tablets[2].Alias, `STOP SLAVE; RESET SLAVE ALL`)
+	err = clusterInstance.VtctlclientProcess.ExecuteCommand("ExecuteFetchAsDba", tablets[2].Alias, `STOP SLAVE;`)
 	require.NoError(t, err)
-
+	err = clusterInstance.VtctlclientProcess.ExecuteCommand("ExecuteFetchAsDba", tablets[3].Alias, `STOP SLAVE SQL_THREAD;`)
+	require.NoError(t, err)
+	// Run an additional command in the current primary which will only be acked by tablets[3] and be in its relay log.
+	insertedVal := utils.ConfirmReplication(t, tablets[0], nil)
+	// Failover to tablets[3]
 	out, err := utils.Ers(clusterInstance, tablets[3], "60s", "30s")
 	require.NoError(t, err, out)
+	// Verify that the tablet has the inserted value
+	err = utils.CheckInsertedValues(context.Background(), t, tablets[3], insertedVal)
+	require.NoError(t, err)
+	// Confirm that replication is setup correctly from tablets[3] to tablets[0]
+	utils.ConfirmReplication(t, tablets[3], tablets[:1])
+	// Confirm that tablets[2] which had replication stopped initially still has its replication stopped
+	utils.CheckReplicationStatus(context.Background(), t, tablets[2], false, false)
 }
 
 // TestERSForInitialization tests whether calling ERS in the beginning sets up the cluster properly or not
diff --git a/go/test/endtoend/reparent/plannedreparent/reparent_test.go b/go/test/endtoend/reparent/plannedreparent/reparent_test.go
index c6800d66507..fcbd9bc523b 100644
--- a/go/test/endtoend/reparent/plannedreparent/reparent_test.go
+++ b/go/test/endtoend/reparent/plannedreparent/reparent_test.go
@@ -287,6 +287,11 @@ func TestReparentWithDownReplica(t *testing.T) {
 	_, err = utils.Prs(t, clusterInstance, tablets[1])
 	require.NoError(t, err)
 
+	// We have to StartReplication on tablets[2] since the MySQL instance is restarted and does not have replication running
+	// We earlier used to rely on replicationManager to fix this but we have disabled it in our testing environment for latest versions of vttablet and vtctl.
+	err = clusterInstance.VtctlclientProcess.ExecuteCommand("StartReplication", tablets[2].Alias)
+	require.NoError(t, err)
+
 	// wait until it gets the data
 	err = utils.CheckInsertedValues(ctx, t, tablets[2], insertVal)
 	require.NoError(t, err)
diff --git a/go/test/endtoend/reparent/utils/utils.go b/go/test/endtoend/reparent/utils/utils.go
index 326e17e7cc6..dd9202c980e 100644
--- a/go/test/endtoend/reparent/utils/utils.go
+++ b/go/test/endtoend/reparent/utils/utils.go
@@ -128,6 +128,15 @@ func setupCluster(ctx context.Context, t *testing.T, shardName string, cells []s
 		// DemotePrimary rpc is stalled!
 		"-queryserver_enable_online_ddl=false",
 	}
+	if clusterInstance.VtTabletMajorVersion >= 13 && clusterInstance.VtctlMajorVersion >= 13 {
+		// disabling active reparents on the tablet since we don't want the replication manager
+		// to fix replication if it is stopped. Some tests deliberately do that. Also, we don't want
+		// the replication manager to silently fix the replication in case ERS or PRS mess up. All the
+		// tests in this test suite should work irrespective of this flag. Each run of ERS, PRS should be
+		// setting up the replication correctly.
+		// However, due to the bugs in old vitess components we can only do this for version >= 13.
+		clusterInstance.VtTabletExtraArgs = append(clusterInstance.VtTabletExtraArgs, "-disable_active_reparents")
+	}
 
 	// Initialize Cluster
 	err = clusterInstance.SetupCluster(keyspace, []cluster.Shard{*shard})
@@ -607,3 +616,19 @@ func SetReplicationSourceFailed(tablet *cluster.Vttablet, prsOut string) bool {
 	}
 	return strings.Contains(prsOut, fmt.Sprintf("tablet %s failed to SetMaster", tablet.Alias))
 }
+
+// CheckReplicationStatus checks that the replication for sql and io threads is setup as expected
+func CheckReplicationStatus(ctx context.Context, t *testing.T, tablet *cluster.Vttablet, sqlThreadRunning bool, ioThreadRunning bool) {
+	res := RunSQL(ctx, t, "show slave status;", tablet)
+	if ioThreadRunning {
+		require.Equal(t, "Yes", res.Rows[0][10].ToString())
+	} else {
+		require.Equal(t, "No", res.Rows[0][10].ToString())
+	}
+
+	if sqlThreadRunning {
+		require.Equal(t, "Yes", res.Rows[0][11].ToString())
+	} else {
+		require.Equal(t, "No", res.Rows[0][11].ToString())
+	}
+}
diff --git a/go/vt/mysqlctl/replication.go b/go/vt/mysqlctl/replication.go
index 61f24fdfc5b..844700909de 100644
--- a/go/vt/mysqlctl/replication.go
+++ b/go/vt/mysqlctl/replication.go
@@ -244,6 +244,14 @@ func (mysqld *Mysqld) WaitSourcePos(ctx context.Context, targetPos mysql.Positio
 			return nil
 		}
 
+		// Start the SQL Thread before waiting for position to be reached, since the replicas
+		// can only make forward progress if the SQL thread is started and we have already verified
+		// that the replica is not already as advanced as we want it to be
+		err = mysqld.executeSuperQueryListConn(ctx, conn, []string{conn.StartSQLThreadCommand()})
+		if err != nil {
+			return err
+		}
+
 		// Find the query to run, run it.
 		query, err = conn.WaitUntilPositionCommand(ctx, targetPos)
 		if err != nil {