diff --git a/nixos/modules/tasks/filesystems/envfs.nix b/nixos/modules/tasks/filesystems/envfs.nix
index 1e821277b614..4b1846f5c1a8 100644
--- a/nixos/modules/tasks/filesystems/envfs.nix
+++ b/nixos/modules/tasks/filesystems/envfs.nix
@@ -74,5 +74,39 @@ in
     # We no longer need those when using envfs
     system.activationScripts.usrbinenv = lib.mkForce "";
     system.activationScripts.binsh = lib.mkForce "";
+
+    # Disabling the activation scripts above prevents the creation of 2
+    # directories, which would normally be created just before switch-root at
+    # stage1. This causes problems when systemd is used in the initrd.
+    #
+    # This only affects fresh installations or systems using impermanence/tmpfs
+    # root, where these directories don't persist from a previous activation.
+    boot.initrd.systemd.tmpfiles.settings = lib.mkIf config.boot.initrd.systemd.enable {
+      "50-envfs" = {
+        # During switch-root, systemd's base_filesystem_create_fd() creates an
+        # empty /usr. Later at stage2, systemd initialize_runtime() checks
+        # dir_is_empty("/usr/"), which returns 1 for an empty but existing
+        # directory causing a fatal boot failure: "Refusing to run in
+        # unsupported environment where /usr/ is not populated."
+        "/sysroot/usr/bin" = {
+          d = {
+            group = "root";
+            mode = "0755";
+            user = "root";
+          };
+        };
+        # During switch-root, base_filesystem_create_fd() creates a symlink
+        # /bin -> /usr/bin if /bin does not exist. systemd-fstab-generator then
+        # canonicalizes the /bin fstab entry through this symlink, producing a
+        # duplicate usr-bin.mount. Create /bin to avoid this behaviour.
+        "/sysroot/bin" = {
+          d = {
+            group = "root";
+            mode = "0755";
+            user = "root";
+          };
+        };
+      };
+    };
   };
 }
diff --git a/nixos/tests/all-tests.nix b/nixos/tests/all-tests.nix
index 7892274095aa..99c1d26f6f34 100644
--- a/nixos/tests/all-tests.nix
+++ b/nixos/tests/all-tests.nix
@@ -518,7 +518,14 @@ in
   enlightenment = runTest ./enlightenment.nix;
   ente = runTest ./ente;
   env = runTest ./env.nix;
-  envfs = runTest ./envfs.nix;
+  envfs = runTest {
+    imports = [ ./envfs.nix ];
+    _module.args.systemdStage1 = false;
+  };
+  envfs-systemd-stage-1 = runTest {
+    imports = [ ./envfs.nix ];
+    _module.args.systemdStage1 = true;
+  };
   envoy = runTest {
     imports = [ ./envoy.nix ];
     _module.args.envoyPackage = pkgs.envoy;
diff --git a/nixos/tests/envfs.nix b/nixos/tests/envfs.nix
index 6e8ee7e55aea..78946285ed68 100644
--- a/nixos/tests/envfs.nix
+++ b/nixos/tests/envfs.nix
@@ -1,4 +1,9 @@
-{ lib, pkgs, ... }:
+{
+  pkgs,
+  systemdStage1 ? false,
+  ...
+}:
+
 let
   pythonShebang = pkgs.writeScript "python-shebang" ''
     #!/usr/bin/python
@@ -12,7 +17,11 @@ let
 in
 {
   name = "envfs";
-  nodes.machine.services.envfs.enable = true;
+
+  nodes.machine = {
+    services.envfs.enable = true;
+    boot.initrd.systemd.enable = systemdStage1;
+  };
 
   testScript = ''
     start_all()
diff --git a/pkgs/by-name/en/envfs/package.nix b/pkgs/by-name/en/envfs/package.nix
index 7e2fbd3127d3..f1601aa562bc 100644
--- a/pkgs/by-name/en/envfs/package.nix
+++ b/pkgs/by-name/en/envfs/package.nix
@@ -25,7 +25,7 @@ rustPlatform.buildRustPackage (finalAttrs: {
 
   passthru = {
     tests = {
-      envfs = nixosTests.envfs;
+      inherit (nixosTests) envfs envfs-systemd-stage-1;
     };
 
     updateScript = nix-update-script { };