diff --git a/nixos/modules/services/misc/nix-daemon.nix b/nixos/modules/services/misc/nix-daemon.nix
index 09a874481dc..4bfd6268234 100644
--- a/nixos/modules/services/misc/nix-daemon.nix
+++ b/nixos/modules/services/misc/nix-daemon.nix
@@ -342,8 +342,7 @@ in
           /nix/var/nix/profiles \
           /nix/var/nix/db \
           /nix/var/log/nix/drvs \
-          /nix/var/nix/channel-cache \
-          /nix/var/nix/chroots
+          /nix/var/nix/channel-cache
         mkdir -m 1777 -p \
           /nix/var/nix/gcroots/per-user \
           /nix/var/nix/profiles/per-user \
diff --git a/nixos/modules/system/boot/stage-2-init.sh b/nixos/modules/system/boot/stage-2-init.sh
index 62e08bb9ece..cee9db091c1 100644
--- a/nixos/modules/system/boot/stage-2-init.sh
+++ b/nixos/modules/system/boot/stage-2-init.sh
@@ -104,12 +104,6 @@ if test -n "@cleanTmpDir@"; then
     echo " done"
 fi
 
-# This is a good time to clean up /nix/var/nix/chroots.  Doing an `rm
-# -rf' on it isn't safe in general because it can contain bind mounts
-# to /nix/store and other places.  But after rebooting these are all
-# gone, of course.
-rm -rf /nix/var/nix/chroots # recreated in activate-configuration.sh
-
 
 # Also get rid of temporary GC roots.
 rm -rf /nix/var/nix/gcroots/tmp /nix/var/nix/temproots