diff --git a/src/backend/bootstrap/bootstrap.c b/src/backend/bootstrap/bootstrap.c
index fc8638c1b61..facad43c74c 100644
--- a/src/backend/bootstrap/bootstrap.c
+++ b/src/backend/bootstrap/bootstrap.c
@@ -220,6 +220,9 @@ BootstrapModeMain(int argc, char *argv[], bool check_only)
 	argv++;
 	argc--;
 
+	SetProcessingMode(BootstrapProcessing);
+	IgnoreSystemIndexes = true;
+
 	while ((flag = getopt(argc, argv, "B:c:d:D:Fkr:X:-:")) != -1)
 	{
 		switch (flag)
@@ -321,9 +324,6 @@ BootstrapModeMain(int argc, char *argv[], bool check_only)
 
 	CreateDataDirLockFile(false);
 
-	SetProcessingMode(BootstrapProcessing);
-	IgnoreSystemIndexes = true;
-
 	InitializeMaxBackends();
 
 	/*
diff --git a/src/backend/utils/misc/guc.c b/src/backend/utils/misc/guc.c
index 667df448732..9555b363c34 100644
--- a/src/backend/utils/misc/guc.c
+++ b/src/backend/utils/misc/guc.c
@@ -3464,6 +3464,15 @@ set_config_with_handle(const char *name, config_handle *handle,
 		return 0;
 	}
 
+	/*
+	 * Certain GUCs aren't safe to enable during bootstrap mode.  Silently
+	 * ignore attempts to set them to non-default values.
+	 */
+	if (unlikely(IsBootstrapProcessingMode()) &&
+		strcmp(record->name, "transaction_timeout") == 0 &&
+		source != PGC_S_DEFAULT)
+		changeVal = false;
+
 	/*
 	 * Check if the option can be set at this time. See guc.h for the precise
 	 * rules.