diff --git a/payu/experiment.py b/payu/experiment.py
index e0a06706..c66e8845 100644
--- a/payu/experiment.py
+++ b/payu/experiment.py
@@ -28,6 +28,7 @@
 from payu import envmod
 from payu.fsops import mkdir_p, make_symlink, read_config, movetree
 from payu.fsops import list_archive_dirs
+from payu.fsops import run_script_command
 from payu.schedulers.pbs import get_job_info, pbs_env_init, get_job_id
 from payu.models import index as model_index
 import payu.profilers
@@ -887,44 +888,12 @@ def set_userscript_env_vars(self):
             }
         )
 
-    def run_userscript(self, script_cmd):
-        # Setup environment variables with current run information
+    def run_userscript(self, script_cmd : str):
+        """Run a user defined script or subcommand at various stages of the
+        payu submissions"""
         self.set_userscript_env_vars()
-
-        # First try to interpret the argument as a full command:
-        try:
-            sp.check_call(shlex.split(script_cmd))
-        except EnvironmentError as exc:
-            # Now try to run the script explicitly
-            if exc.errno == errno.ENOENT:
-                cmd = os.path.join(self.control_path, script_cmd)
-                # Simplistic recursion check
-                assert os.path.isfile(cmd)
-                self.run_userscript(cmd)
-
-            # If we get a "non-executable" error, then guess the type
-            elif exc.errno == errno.EACCES:
-                # TODO: Move outside
-                ext_cmd = {'.py': sys.executable,
-                           '.sh': '/bin/bash',
-                           '.csh': '/bin/tcsh'}
-
-                _, f_ext = os.path.splitext(script_cmd)
-                shell_name = ext_cmd.get(f_ext)
-                if shell_name:
-                    print('payu: warning: Assuming that {0} is a {1} script '
-                          'based on the filename extension.'
-                          ''.format(os.path.basename(script_cmd),
-                                    os.path.basename(shell_name)))
-                    cmd = ' '.join([shell_name, script_cmd])
-                    self.run_userscript(cmd)
-                else:
-                    # If we can't guess the shell, then abort
-                    raise
-        except sp.CalledProcessError as exc:
-            # If the script runs but the output is bad, then warn the user
-            print('payu: warning: user script \'{0}\' failed (error {1}).'
-                  ''.format(script_cmd, exc.returncode))
+        run_script_command(script_cmd,
+                           control_path=Path(self.control_path))
 
     def sweep(self, hard_sweep=False):
         # TODO: Fix the IO race conditions!
diff --git a/payu/fsops.py b/payu/fsops.py
index cc1c09f7..8d480929 100644
--- a/payu/fsops.py
+++ b/payu/fsops.py
@@ -27,6 +27,11 @@
 # Delete this once this bug in Lustre is fixed
 CHECK_LUSTRE_PATH_LEN = True
 
+# File extensions to script interpreters
+EXTENSION_TO_INTERPRETER = {'.py': sys.executable,
+                            '.sh': '/bin/bash',
+                            '.csh': '/bin/tcsh'}
+
 
 def mkdir_p(path):
     """Create a new directory; ignore if it already exists."""
@@ -229,3 +234,91 @@ def list_archive_dirs(archive_path: Union[Path, str],
 
     dirs.sort(key=lambda d: int(d.lstrip(dir_type)))
     return dirs
+
+
+def run_script_command(script_cmd: str, control_path: Path) -> None:
+    """Run a user defined script or command.
+
+    Parameters
+    ----------
+    script_cmd : string
+        String of user-script command defined in configuration file
+    control_path : Path
+        The control directory of the experiment
+
+    Raises
+    ------
+    RuntimeError
+        If there's was an error running the user-script
+    """
+    try:
+        _run_script(script_cmd, control_path)
+    except Exception as e:
+        error_msg = f"User defined script/command failed to run: {script_cmd}"
+        raise RuntimeError(error_msg) from e
+
+def needs_subprocess_shell(command: str) -> bool:
+    """Check if command contains shell specific values. For example, file
+    redirections, pipes or logical operators.
+
+    Parameters
+    ----------
+    command: string
+        String of command to run in subprocess call
+
+    Returns
+    -------
+    bool
+        Returns True if command requires a subprocess shell, False otherwise
+    """
+    shell_values = ['>', '<', '|', '&&', '$', '`']
+    for value in shell_values:
+        if value in command:
+            return True
+    return False
+
+def _run_script(script_cmd: str, control_path: Path) -> None:
+    """Helper recursive function to attempt running a script command.
+
+    Parameters
+    ----------
+    script_cmd : string
+        The script command to attempt to run in subprocess call
+    control_path: Path
+        The control directory to use for resolving relative filepaths, if file
+        is not found
+    """
+    # First try to interpret the argument as a full command:
+    try:
+        if needs_subprocess_shell(script_cmd):
+            subprocess.check_call(script_cmd, shell=True)
+        else:
+            subprocess.check_call(shlex.split(script_cmd))
+    except EnvironmentError as e:
+        # Now try to run the script explicitly
+        if e.errno == errno.ENOENT:
+            # Check if script is a file in the control directory
+            cmd = control_path / script_cmd
+            if cmd.is_file():
+                _run_script(str(cmd), control_path)
+            else:
+                raise
+
+        # If we get a "non-executable" error, then guess the type
+        elif e.errno == errno.EACCES:
+            _, file_ext = os.path.splitext(script_cmd)
+            shell_name = EXTENSION_TO_INTERPRETER.get(file_ext, None)
+            if shell_name:
+                print('payu: warning: Assuming that {0} is a {1} '
+                      'script based on the filename extension.'
+                      ''.format(os.path.basename(script_cmd),
+                                os.path.basename(shell_name)))
+
+                cmd = f'{shell_name} {script_cmd}'
+                _run_script(cmd, control_path)
+            else:
+                raise
+
+        # Otherwise re-raise the error
+        else:
+            raise
diff --git a/test/test_payu.py b/test/test_payu.py
index b1184fc5..5b4beac8 100644
--- a/test/test_payu.py
+++ b/test/test_payu.py
@@ -12,7 +12,7 @@
 import payu.laboratory
 import payu.envmod
 
-from .common import testdir, tmpdir, ctrldir, labdir, workdir
+from .common import testdir, tmpdir, ctrldir, labdir, workdir, cd
 from .common import make_exe, make_inputs, make_restarts, make_all_files
 
 
@@ -301,3 +301,116 @@ def test_list_archive_dirs():
     # Clean up test archive
     shutil.rmtree(tmp_archive)
     shutil.rmtree(tmp_archive_2)
+
+
+@pytest.fixture
+def script_control_dir():
+    # Create a temporary control directory
+    control_dir = tmpdir / 'script_control_dir'
+    control_dir.mkdir()
+
+    yield control_dir
+
+    # Tear down
+    shutil.rmtree(control_dir)
+
+
+def test_run_userscript_python_script(script_control_dir: Path):
+    # Create a simple python script
+    python_script = script_control_dir / 'test_script.py'
+    with open(python_script, 'w') as f:
+        f.writelines([
+            f"with open('{script_control_dir}/output.txt', 'w') as f:\n",
+            "   f.write('Test Python user script')"
+        ])
+
+    # Test run userscript
+    payu.fsops.run_script_command('test_script.py', script_control_dir)
+
+    # Check script output
+    with open((script_control_dir / 'output.txt'), 'r') as f:
+        assert f.read() == "Test Python user script"
+
+
+def test_run_userscript_bash_script(script_control_dir: Path):
+    # Create a simple bash script
+    bash_script = script_control_dir / 'test_script.sh'
+    with open(bash_script, 'w') as f:
+        f.writelines([
+            '#!/bin/bash\n',
+            'echo -n "Test bash user script" > output.txt'
+        ])
+
+    # Test execute script
+    with cd(script_control_dir):
+        payu.fsops.run_script_command('./test_script.sh', script_control_dir)
+
+    # Check script output
+    with open((script_control_dir / 'output.txt'), 'r') as f:
+        assert f.read() == "Test bash user script"
+
+
+def test_userscript_unknown_extension(script_control_dir: Path):
+    # Create a text file
+    text_file = script_control_dir / 'test_txt.txt'
+    text_file.touch()
+
+    # Test user script raises an error
+    with pytest.raises(RuntimeError):
+        payu.fsops.run_script_command(str(text_file), script_control_dir)
+
+
+def test_userscript_non_existent_file(script_control_dir: Path):
+    # Test user script raises an error
+    with pytest.raises(RuntimeError):
+        payu.fsops.run_script_command('unknown_userscript.sh',
+                                      script_control_dir)
+
+
+def test_userscript_non_existent_file(script_control_dir: Path):
+    # Test userscript raises an error
+    with pytest.raises(RuntimeError):
+        payu.fsops.run_script_command('unknown_userscript.sh',
+                                      script_control_dir)
+
+
+def test_run_userscript_python_script_eror(script_control_dir):
+    # Create a python script that'll exit with an error
+    python_script = script_control_dir / 'test_script.py'
+    with open(python_script, 'w') as f:
+        f.write('raise ValueError("Test that script exits with error")')
+
+    # Test userscript raises an error
+    with pytest.raises(RuntimeError):
+        payu.fsops.run_script_command('test_script.py',
+                                      script_control_dir)
+
+
+def test_run_userscript_command(script_control_dir):
+    # Create a simple command
+    cmd = 'echo -n "some_data" > test.txt'
+
+    # Test payu userscript
+    with cd(script_control_dir):
+        payu.fsops.run_script_command(cmd, script_control_dir)
+
+    # Check userscript output
+    with open((script_control_dir / 'test.txt'), 'r') as f:
+        content = f.read()
+        assert content == "some_data"
+
+
+@pytest.mark.parametrize("command, expected", [
+    ('echo "Some Data" > test.txt', True),
+    ('ls -l | grep "test"', True),
+    ('cmd1 && cmd2', True),
+    ('cmd1 || cmd2', True),
+    ('echo "Data"', False),
+    ('ls -l', False),
+    ('some_python_script.py', False),
+    ('/bin/bash script.sh', False),
+    ('echo $PAYU_ENV_VALUE', True),
+    ('echo `date`', True)
+])
+def test_needs_shell(command, expected):
+    assert payu.fsops.needs_subprocess_shell(command) == expected