diff --git a/nixos/modules/system/boot/loader/limine/limine-install.py b/nixos/modules/system/boot/loader/limine/limine-install.py
index 9add26b636c6..dacf4a339d0e 100644
--- a/nixos/modules/system/boot/loader/limine/limine-install.py
+++ b/nixos/modules/system/boot/loader/limine/limine-install.py
@@ -347,7 +347,7 @@ def config_entry(levels: int, bootspec: BootSpec, label: str, time: str) -> str:
             os.path.basename(bootspec.toplevel) + "-secrets"
         )
 
-        if os.system(bootspec.initrdSecrets + " " + initrd_secrets_path_temp) != 0:
+        if subprocess.run([bootspec.initrdSecrets, initrd_secrets_path_temp]).returncode != 0:
             print(
                 f'warning: failed to create initrd secrets for "{label}"',
                 file=sys.stderr,
diff --git a/pkgs/by-name/mi/microsoft-edge/update.py b/pkgs/by-name/mi/microsoft-edge/update.py
index d2298c382e6f..1e6419338fce 100755
--- a/pkgs/by-name/mi/microsoft-edge/update.py
+++ b/pkgs/by-name/mi/microsoft-edge/update.py
@@ -1,7 +1,7 @@
 #! /usr/bin/env nix-shell
 #! nix-shell -i python3 -p python3Packages.packaging python3Packages.python-debian common-updater-scripts
 
-import os
+import subprocess
 from collections import OrderedDict
 from os.path import abspath, dirname
 from urllib import request
@@ -39,8 +39,8 @@ def write_expression():
     version = Version.re_valid_version.match(latest["stable"]["Version"]).group(
         "upstream_version"
     )
-    os.system(f'update-source-version microsoft-edge "{version}"')
-    os.system(f'update-source-version msedgedriver "{version}"')
+    subprocess.run(["update-source-version", "microsoft-edge", version])
+    subprocess.run(["update-source-version", "msedgedriver", version])
 
 
 write_expression()
diff --git a/pkgs/development/python-modules/courlan/default.nix b/pkgs/development/python-modules/courlan/default.nix
index d3e63da7213b..86da2f43e917 100644
--- a/pkgs/development/python-modules/courlan/default.nix
+++ b/pkgs/development/python-modules/courlan/default.nix
@@ -39,7 +39,7 @@ buildPythonPackage (finalAttrs: {
       substituteInPlace tests/unit_tests.py \
         --replace-fail \
           'assert os.system("courlan --help") == 0' \
-          'assert os.system("${courlanBinPath} --help") == 0' \
+          'assert subprocess.run(["${courlanBinPath}", "--help"]).returncode == 0' \
         --replace-fail \
           'courlan_bin = "courlan"' \
           'courlan_bin = "${courlanBinPath}"'
diff --git a/pkgs/development/python-modules/riscof/make_writeable.patch b/pkgs/development/python-modules/riscof/make_writeable.patch
index 938f9913a7ad..c597338cda00 100644
--- a/pkgs/development/python-modules/riscof/make_writeable.patch
+++ b/pkgs/development/python-modules/riscof/make_writeable.patch
@@ -1,25 +1,33 @@
 diff --git a/riscof/cli.py b/riscof/cli.py
-index 26af62e..9d0ddbf 100644
+index 26af62e..94051ae 100644
 --- a/riscof/cli.py
 +++ b/riscof/cli.py
-@@ -502,6 +502,7 @@ def setup(dutname,refname,work_dir):
+@@ -7,6 +7,7 @@ import os
+ import sys
+ import pytz
+ import shutil
++import subprocess
+ import configparser
+ import distutils.dir_util
+
+@@ -502,6 +503,7 @@ def setup(dutname,refname,work_dir):
          src = os.path.join(constants.root, "Templates/setup/model/")
          dest = os.path.join(cwd, dutname)
          distutils.dir_util.copy_tree(src, dest)
-+        os.system(f"chmod +w -R '{dest}'")
++        subprcess.run(["chmod", "+w", "-R", dest])
  
          os.rename(cwd+'/'+dutname+'/model_isa.yaml',
                  cwd+'/'+dutname+'/'+dutname+'_isa.yaml')
-@@ -525,10 +526,12 @@ def setup(dutname,refname,work_dir):
+@@ -525,10 +527,12 @@ def setup(dutname,refname,work_dir):
              src = os.path.join(constants.root, "Templates/setup/sail_cSim/")
              dest = os.path.join(cwd, refname)
              distutils.dir_util.copy_tree(src, dest)
-+            os.system(f"chmod +w -R '{dest}'")
++            subprcess.run(["chmod", "+w", "-R", dest])
          else:
              src = os.path.join(constants.root, "Templates/setup/reference/")
              dest = os.path.join(cwd, refname)
              distutils.dir_util.copy_tree(src, dest)
-+            os.system(f"chmod +w -R '{dest}'")
++            subprcess.run(["chmod", "+w", "-R", dest])
              os.rename(cwd+'/'+refname+'/riscof_model.py',
                  cwd+'/'+refname+'/riscof_'+refname+'.py')
              with open(cwd+'/'+refname+'/riscof_'+refname+'.py', 'r') as file :