diff --git a/easybuild/tools/run.py b/easybuild/tools/run.py
index 5477e07d2e..8981b6ba41 100644
--- a/easybuild/tools/run.py
+++ b/easybuild/tools/run.py
@@ -273,14 +273,16 @@ def create_cmd_scripts(cmd_str, work_dir, env, tmpdir, out_file, err_file):
     # Make script that sets up bash shell with specified environment and working directory
     cmd_fp = os.path.join(tmpdir, 'cmd.sh')
 
-    # using -i to force interactive shell, so env.sh is also sourced when -c is used to run commands
-    launch_cmd = 'bash --rcfile $EB_SCRIPT_DIR/env.sh -i "$@"'
-
+    launch_cmd = 'bash'
     # prefix launch command with bwrap (if used)
     bwrap_cmd = os.getenv('EB_BWRAP_CMD')
     if bwrap_cmd:
         launch_cmd = bwrap_cmd + ' ' + launch_cmd
 
+    # using -i for interactive shell, so env.sh is sourced
+    launch_cmd_interactive = f'{launch_cmd} --rcfile $EB_SCRIPT_DIR/env.sh -i'
+    launch_cmd_with_args = f'BASH_ENV=$EB_SCRIPT_DIR/env.sh {launch_cmd} "$@"'
+
     with open(cmd_fp, 'w') as fid:
         fid.write('#!/usr/bin/env bash\n')
         fid.write('# Run this script to set up a shell environment that EasyBuild used to run the shell command\n')
@@ -288,7 +290,11 @@ def create_cmd_scripts(cmd_str, work_dir, env, tmpdir, out_file, err_file):
             'EB_SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )',
             f'echo "# Shell for the command: \'"{shlex.quote(cmd_str)}"\'"',
             'echo "# Use command history, exit to stop"',
-            launch_cmd,
+            'if [ "$#" -eq 0 ]; then',
+            '  ' + launch_cmd_interactive,
+            'else',
+            '  ' + launch_cmd_with_args,
+            'fi',
         ]))
     os.chmod(cmd_fp, 0o775)
 
diff --git a/test/framework/run.py b/test/framework/run.py
index 5536570a77..59e04c27ae 100644
--- a/test/framework/run.py
+++ b/test/framework/run.py
@@ -266,20 +266,23 @@ def test_run_shell_cmd_basic(self):
         cmd_script = os.path.join(cmd_tmpdir, 'cmd.sh')
         self.assertExists(cmd_script)
 
-        cmd = f"{cmd_script} -c 'echo pwd: $PWD; echo $FOOBAR; echo $EB_CMD_OUT_FILE; cat $EB_CMD_OUT_FILE'"
+        cmd = f"{cmd_script} -c '"
+        cmd += 'echo pwd: $PWD; echo "bash_env: $BASH_ENV"; echo $FOOBAR; echo $EB_CMD_OUT_FILE; cat $EB_CMD_OUT_FILE'
+        cmd += "'"
         with self.mocked_stdout_stderr():
             res = run_shell_cmd(cmd, fail_on_error=False)
         self.assertEqual(res.exit_code, 0)
-        regex = re.compile("pwd: .*\nfoobar\n.*/echo-.*/out.txt\nhello$")
+        regex = re.compile("pwd: .*\nbash_env: .*\nfoobar\n.*/echo-.*/out.txt\nhello$")
         self.assertTrue(regex.search(res.output), f"Pattern '{regex.pattern}' should be found in {res.output}")
 
         # check whether working directory is what's expected
-        regex = re.compile('^pwd: .*', re.M)
-        res = regex.findall(res.output)
-        self.assertEqual(len(res), 1)
-        pwd = res[0].strip()[5:]
+        matches = re.findall('^pwd: (.*)', res.output, re.M)
+        self.assertEqual(len(matches), 1)
+        pwd = matches[0]
         self.assertTrue(os.path.samefile(pwd, self.test_prefix))
 
+        # BASH_ENV is that of the current shell, not the one set in the cmd.sh
+        self.assertEqual(re.search('^bash_env: (.*)', res.output, re.M)[1], os.environ.get('BASH_ENV', ''))
         cmd = f"{cmd_script} -c 'module --version'"
         with self.mocked_stdout_stderr():
             res = run_shell_cmd(cmd, fail_on_error=False)