diff --git a/nixos/modules/virtualisation/nixos-container.pl b/nixos/modules/virtualisation/nixos-container.pl
index 5083abd84489..c0d30346e568 100644
--- a/nixos/modules/virtualisation/nixos-container.pl
+++ b/nixos/modules/virtualisation/nixos-container.pl
@@ -152,6 +152,7 @@ if ($action eq "create") {
 
 my $root = "/var/lib/containers/$containerName";
 my $profileDir = "/nix/var/nix/profiles/per-container/$containerName";
+my $gcRootsDir = "/nix/var/nix/gcroots/per-container/$containerName";
 my $confFile = "/etc/containers/$containerName.conf";
 die "$0: container ‘$containerName’ does not exist\n" if !-e $confFile;
 
@@ -172,6 +173,7 @@ if ($action eq "destroy") {
     stopContainer if isContainerRunning;
 
     rmtree($profileDir) if -e $profileDir;
+    rmtree($gcRootsDir) if -e $gcRootsDir;
     rmtree($root) if -e $root;
     unlink($confFile) or die;
 }