diff --git a/nixos/modules/services/misc/nix-daemon.nix b/nixos/modules/services/misc/nix-daemon.nix
index 4bfd6268234d..171fd08f1e1d 100644
--- a/nixos/modules/services/misc/nix-daemon.nix
+++ b/nixos/modules/services/misc/nix-daemon.nix
@@ -336,13 +336,13 @@ in
         # Nix initialisation.
         mkdir -m 0755 -p \
           /nix/var/nix/gcroots \
-          /nix/var/nix/temproots \
           /nix/var/nix/manifests \
-          /nix/var/nix/userpool \
           /nix/var/nix/profiles \
           /nix/var/nix/db \
           /nix/var/log/nix/drvs \
-          /nix/var/nix/channel-cache
+          /nix/var/nix/channel-cache \
+          /run/nix/temproots \
+          /run/nix/userpool
         mkdir -m 1777 -p \
           /nix/var/nix/gcroots/per-user \
           /nix/var/nix/profiles/per-user \
@@ -350,6 +350,9 @@ in
 
         ln -sf /nix/var/nix/profiles /nix/var/nix/gcroots/
         ln -sf /nix/var/nix/manifests /nix/var/nix/gcroots/
+
+        [ -d /nix/var/nix/temproots ] || ln -sfn /run/nix/temproots /nix/var/nix/temproots
+        [ -d /nix/var/nix/userpool ] || ln -sfn /run/nix/userpool /nix/var/nix/userpool
       '';
 
   };
diff --git a/nixos/modules/system/boot/stage-2-init.sh b/nixos/modules/system/boot/stage-2-init.sh
index cee9db091c14..5be38725ab72 100644
--- a/nixos/modules/system/boot/stage-2-init.sh
+++ b/nixos/modules/system/boot/stage-2-init.sh
@@ -106,7 +106,7 @@ fi
 
 
 # Also get rid of temporary GC roots.
-rm -rf /nix/var/nix/gcroots/tmp /nix/var/nix/temproots
+rm -rf /nix/var/nix/gcroots/tmp /nix/var/nix/temproots /nix/var/nix/userpool
 
 
 # Create a tmpfs on /run to hold runtime state for programs such as