diff --git a/doc/command-line-flags.md b/doc/command-line-flags.md
index dd8f1cd74..cf2b2ca95 100644
--- a/doc/command-line-flags.md
+++ b/doc/command-line-flags.md
@@ -202,10 +202,6 @@ List of metrics and threshold values; topping the threshold of any will cause th
 
 Typically `gh-ost` is used to migrate tables on a master. If you wish to only perform the migration in full on a replica, connect `gh-ost` to said replica and pass `--migrate-on-replica`. `gh-ost` will briefly connect to the master but otherwise will make no changes on the master. Migration will be fully executed on the replica, while making sure to maintain a small replication lag.
 
-### mysql-wait-timeout
-
-If set to a value greater than zero, causes `gh-ost` to set a provided [MySQL `wait_timeout`](https://dev.mysql.com/doc/refman/8.0/en/server-system-variables.html#sysvar_wait_timeout) for MySQL sessions opened by `gh-ost`, specified in seconds.
-
 ### postpone-cut-over-flag-file
 
 Indicate a file name, such that the final [cut-over](cut-over.md) step does not take place as long as the file exists.
diff --git a/go/base/context.go b/go/base/context.go
index 41baae696..59227ea2d 100644
--- a/go/base/context.go
+++ b/go/base/context.go
@@ -164,6 +164,7 @@ type MigrationContext struct {
 	Hostname                               string
 	AssumeMasterHostname                   string
 	ApplierTimeZone                        string
+	ApplierWaitTimeout                     int64
 	TableEngine                            string
 	RowsEstimate                           int64
 	RowsDeltaEstimate                      int64
diff --git a/go/cmd/gh-ost/main.go b/go/cmd/gh-ost/main.go
index 39c815bc8..3e6057995 100644
--- a/go/cmd/gh-ost/main.go
+++ b/go/cmd/gh-ost/main.go
@@ -51,7 +51,6 @@ func main() {
 	flag.StringVar(&migrationContext.AssumeMasterHostname, "assume-master-host", "", "(optional) explicitly tell gh-ost the identity of the master. Format: some.host.com[:port] This is useful in master-master setups where you wish to pick an explicit master, or in a tungsten-replicator where gh-ost is unable to determine the master")
 	flag.IntVar(&migrationContext.InspectorConnectionConfig.Key.Port, "port", 3306, "MySQL port (preferably a replica, not the master)")
 	flag.Float64Var(&migrationContext.InspectorConnectionConfig.Timeout, "mysql-timeout", 0.0, "Connect, read and write timeout for MySQL")
-	flag.Float64Var(&migrationContext.InspectorConnectionConfig.WaitTimeout, "mysql-wait-timeout", 0.0, "wait_timeout for MySQL sessions")
 	flag.StringVar(&migrationContext.CliUser, "user", "", "MySQL user")
 	flag.StringVar(&migrationContext.CliPassword, "password", "", "MySQL password")
 	flag.StringVar(&migrationContext.CliMasterUser, "master-user", "", "MySQL user on master, if different from that on replica. Requires --assume-master-host")
diff --git a/go/logic/applier.go b/go/logic/applier.go
index 9b190919f..990fbe720 100644
--- a/go/logic/applier.go
+++ b/go/logic/applier.go
@@ -89,7 +89,7 @@ func (this *Applier) InitDBConnections() (err error) {
 		return err
 	}
 	this.migrationContext.ApplierMySQLVersion = version
-	if err := this.validateAndReadTimeZone(); err != nil {
+	if err := this.validateAndReadGlobalVariables(); err != nil {
 		return err
 	}
 	if !this.migrationContext.AliyunRDS && !this.migrationContext.GoogleCloudPlatform && !this.migrationContext.AzureMySQL {
@@ -106,10 +106,13 @@ func (this *Applier) InitDBConnections() (err error) {
 	return nil
 }
 
-// validateAndReadTimeZone potentially reads server time-zone
-func (this *Applier) validateAndReadTimeZone() error {
-	query := `select /* gh-ost */ @@global.time_zone`
-	if err := this.db.QueryRow(query).Scan(&this.migrationContext.ApplierTimeZone); err != nil {
+// validateAndReadGlobalVariables potentially reads server global variables, such as the time_zone and wait_timeout.
+func (this *Applier) validateAndReadGlobalVariables() error {
+	query := `select /* gh-ost */ @@global.time_zone, @@global.wait_timeout`
+	if err := this.db.QueryRow(query).Scan(
+		&this.migrationContext.ApplierTimeZone,
+		&this.migrationContext.ApplierWaitTimeout,
+	); err != nil {
 		return err
 	}
 
@@ -934,6 +937,27 @@ func (this *Applier) CreateAtomicCutOverSentryTable() error {
 	return nil
 }
 
+// InitAtomicCutOverWaitTimeout sets the cut-over session wait_timeout in order to reduce the
+// time an unresponsive (but still connected) gh-ost process can hold the cut-over lock.
+func (this *Applier) InitAtomicCutOverWaitTimeout(tx *gosql.Tx) error {
+	cutOverWaitTimeoutSeconds := this.migrationContext.CutOverLockTimeoutSeconds * 3
+	this.migrationContext.Log.Infof("Setting cut-over idle timeout as %d seconds", cutOverWaitTimeoutSeconds)
+	query := fmt.Sprintf(`set /* gh-ost */ session wait_timeout:=%d`, cutOverWaitTimeoutSeconds)
+	_, err := tx.Exec(query)
+	return err
+}
+
+// RevertAtomicCutOverWaitTimeout restores the original wait_timeout for the applier session post-cut-over.
+func (this *Applier) RevertAtomicCutOverWaitTimeout() {
+	this.migrationContext.Log.Infof("Reverting cut-over idle timeout to %d seconds", this.migrationContext.ApplierWaitTimeout)
+	query := fmt.Sprintf(`set /* gh-ost */ session wait_timeout:=%d`, this.migrationContext.ApplierWaitTimeout)
+	if _, err := sqlutils.ExecNoPrepare(this.db, query); err != nil {
+		this.migrationContext.Log.Errorf("Failed to restore applier wait_timeout to %d seconds: %v",
+			this.migrationContext.ApplierWaitTimeout, err,
+		)
+	}
+}
+
 // AtomicCutOverMagicLock
 func (this *Applier) AtomicCutOverMagicLock(sessionIdChan chan int64, tableLocked chan<- error, okToUnlockTable <-chan bool, tableUnlocked chan<- error) error {
 	tx, err := this.db.Begin()
@@ -979,6 +1003,12 @@ func (this *Applier) AtomicCutOverMagicLock(sessionIdChan chan int64, tableLocke
 		return err
 	}
 
+	if err := this.InitAtomicCutOverWaitTimeout(tx); err != nil {
+		tableLocked <- err
+		return err
+	}
+	defer this.RevertAtomicCutOverWaitTimeout()
+
 	query = fmt.Sprintf(`lock /* gh-ost */ tables %s.%s write, %s.%s write`,
 		sql.EscapeName(this.migrationContext.DatabaseName),
 		sql.EscapeName(this.migrationContext.OriginalTableName),
diff --git a/go/mysql/connection.go b/go/mysql/connection.go
index 7db51afe4..33bde2b62 100644
--- a/go/mysql/connection.go
+++ b/go/mysql/connection.go
@@ -31,7 +31,6 @@ type ConnectionConfig struct {
 	Timeout              float64
 	TransactionIsolation string
 	Charset              string
-	WaitTimeout          float64
 }
 
 func NewConnectionConfig() *ConnectionConfig {
@@ -52,7 +51,6 @@ func (this *ConnectionConfig) DuplicateCredentials(key InstanceKey) *ConnectionC
 		Timeout:              this.Timeout,
 		TransactionIsolation: this.TransactionIsolation,
 		Charset:              this.Charset,
-		WaitTimeout:          this.WaitTimeout,
 	}
 	config.ImpliedKey = &config.Key
 	return config
@@ -141,9 +139,6 @@ func (this *ConnectionConfig) GetDBUri(databaseName string) string {
 		fmt.Sprintf("readTimeout=%fs", this.Timeout),
 		fmt.Sprintf("writeTimeout=%fs", this.Timeout),
 	}
-	if this.WaitTimeout > 0 {
-		connectionParams = append(connectionParams, fmt.Sprintf("wait_timeout=%fs", this.WaitTimeout))
-	}
 
 	return fmt.Sprintf("%s:%s@tcp(%s:%d)/%s?%s", this.User, this.Password, hostname, this.Key.Port, databaseName, strings.Join(connectionParams, "&"))
 }
diff --git a/go/mysql/connection_test.go b/go/mysql/connection_test.go
index 6398e0169..cc2271f1d 100644
--- a/go/mysql/connection_test.go
+++ b/go/mysql/connection_test.go
@@ -82,7 +82,6 @@ func TestGetDBUri(t *testing.T) {
 	c.User = "gromit"
 	c.Password = "penguin"
 	c.Timeout = 1.2345
-	c.WaitTimeout = 0 // should be ignored
 	c.TransactionIsolation = transactionIsolation
 	c.Charset = "utf8mb4,utf8,latin1"
 
@@ -96,11 +95,10 @@ func TestGetDBUriWithTLSSetup(t *testing.T) {
 	c.User = "gromit"
 	c.Password = "penguin"
 	c.Timeout = 1.2345
-	c.WaitTimeout = 60
 	c.tlsConfig = &tls.Config{}
 	c.TransactionIsolation = transactionIsolation
 	c.Charset = "utf8mb4_general_ci,utf8_general_ci,latin1"
 
 	uri := c.GetDBUri("test")
-	test.S(t).ExpectEquals(uri, `gromit:penguin@tcp(myhost:3306)/test?autocommit=true&interpolateParams=true&charset=utf8mb4_general_ci,utf8_general_ci,latin1&tls=ghost&transaction_isolation="REPEATABLE-READ"&timeout=1.234500s&readTimeout=1.234500s&writeTimeout=1.234500s&wait_timeout=60.000000s`)
+	test.S(t).ExpectEquals(uri, `gromit:penguin@tcp(myhost:3306)/test?autocommit=true&interpolateParams=true&charset=utf8mb4_general_ci,utf8_general_ci,latin1&tls=ghost&transaction_isolation="REPEATABLE-READ"&timeout=1.234500s&readTimeout=1.234500s&writeTimeout=1.234500s`)
 }