diff --git a/share/github-backup-utils/ghe-restore-mysql b/share/github-backup-utils/ghe-restore-mysql
index 9b368d94c..066d23a34 100755
--- a/share/github-backup-utils/ghe-restore-mysql
+++ b/share/github-backup-utils/ghe-restore-mysql
@@ -27,7 +27,7 @@ ghe_remote_version_required "$GHE_HOSTNAME"
 export GHE_RESTORE_SNAPSHOT
 
 # The directory holding the snapshot to restore
-snapshot_dir="$GHE_DATA_DIR/$GHE_RESTORE_SNAPSHOT"
+GHE_RESTORE_SNAPSHOT_PATH="$GHE_DATA_DIR/$GHE_RESTORE_SNAPSHOT"
 
 if is_external_database_snapshot; then
   if [ -n "$EXTERNAL_DATABASE_RESTORE_SCRIPT" ]; then
@@ -40,7 +40,7 @@ if is_external_database_snapshot; then
     bm_end "$(basename $0)"
     exit 0
   else
-    if is_binary_backup "$snapshot_dir"; then
+    if is_binary_backup "$GHE_RESTORE_SNAPSHOT_PATH"; then
       echo "Error: Restore of a binary backup to appliance with an external database configured is not supported."
       echo "Please provide a custom external database restore script with EXTERNAL_DATABASE_RESTORE_SCRIPT"
       exit 1
@@ -63,18 +63,22 @@ if is_external_database_snapshot; then
 fi
 
 if is_binary_backup_feature_on; then
+  # Always restore the password pepper here since it is tied to the MySQL data.
+  restore-secret "password pepper" "password-pepper" "secrets.github.user-password-secrets"
   # Feature "mysql.backup.binary" is on, which means new backup scripts are available
-  if is_binary_backup "$snapshot_dir"; then
+  if is_binary_backup "$GHE_RESTORE_SNAPSHOT_PATH"; then
     ghe-restore-mysql-binary $GHE_HOSTNAME
   else
     ghe-restore-mysql-logical $GHE_HOSTNAME
   fi
 else
   # We do not allow to restore binary backup without "mysql.backup.binary" set
-  if is_binary_backup "$snapshot_dir"; then
+  if is_binary_backup "$GHE_RESTORE_SNAPSHOT_PATH"; then
     echo "To restore from a binary backup, you have to set ghe-config \"mysql.backup.binary\" to true" >&2
     exit 2
   else
+    # Always restore the password pepper here since it is tied to the MySQL data.
+    restore-secret "password pepper" "password-pepper" "secrets.github.user-password-secrets"
     if is_default_external_database_snapshot; then
       ghe-restore-mysql-logical $GHE_HOSTNAME
     else
diff --git a/share/github-backup-utils/ghe-restore-settings b/share/github-backup-utils/ghe-restore-settings
index 5edafc4cb..63dc7aa45 100755
--- a/share/github-backup-utils/ghe-restore-settings
+++ b/share/github-backup-utils/ghe-restore-settings
@@ -40,8 +40,6 @@ restore-secret "external MySQL password" "external-mysql-password" "secrets.exte
 
 # Restore management console password hash if present.
 restore-secret "management console password" "manage-password" "secrets.manage"
-# Restore password pepper if present
-restore-secret "password pepper" "password-pepper" "secrets.github.user-password-secrets"
 
 # Restore SAML keys if present.
 if [ -f "$GHE_RESTORE_SNAPSHOT_PATH/saml-keys.tar" ]; then