diff --git a/nixos/modules/installer/tools/nixos-generate-config.pl b/nixos/modules/installer/tools/nixos-generate-config.pl
index ae09839d071d..1038fadec37d 100644
--- a/nixos/modules/installer/tools/nixos-generate-config.pl
+++ b/nixos/modules/installer/tools/nixos-generate-config.pl
@@ -49,6 +49,7 @@ if (-e "/etc/nixos-generate-config.conf") {
         $rootDir = File::Spec->rel2abs($rootDir); # resolve absolute path
     }
     $kernel = $cfg->val("Defaults", "Kernel") // $kernel;
+    $flake = $cfg->val("Defaults", "Flake") // $flake;
 }
 
 for (my $n = 0; $n < scalar @ARGV; $n++) {
diff --git a/nixos/tests/nixos-generate-config.nix b/nixos/tests/nixos-generate-config.nix
index c887403bbda3..175849bcac62 100644
--- a/nixos/tests/nixos-generate-config.nix
+++ b/nixos/tests/nixos-generate-config.nix
@@ -46,5 +46,11 @@
     machine.succeed("rm -rf /etc/nixos")
     machine.succeed("nixos-generate-config --flake")
     machine.succeed("nix-instantiate --parse /etc/nixos/flake.nix /etc/nixos/configuration.nix /etc/nixos/hardware-configuration.nix")
+
+    machine.succeed("mv /etc/nixos /etc/nixos-with-flake-arg")
+    machine.succeed("printf '[Defaults]\nFlake = 1\n' > /etc/nixos-generate-config.conf")
+    machine.succeed("nixos-generate-config")
+    machine.succeed("nix-instantiate --parse /etc/nixos/flake.nix /etc/nixos/configuration.nix /etc/nixos/hardware-configuration.nix")
+    machine.succeed("diff -r /etc/nixos /etc/nixos-with-flake-arg")
   '';
 }