diff --git a/easybuild/scripts/rpath_args.py b/easybuild/scripts/rpath_args.py
index 611c6a414c..b1831dfb42 100755
--- a/easybuild/scripts/rpath_args.py
+++ b/easybuild/scripts/rpath_args.py
@@ -27,7 +27,9 @@
 Utility script used by RPATH wrapper script;
 output is statements that define the following environment variables
 * $CMD_ARGS: new list of command line arguments to pass
-* $RPATH_ARGS: command line option to specify list of paths to RPATH
+
+Usage:
+    rpath_args.py <cmd> <rpath_filter> <rpath_include> <args...>
 
 author: Kenneth Hoste (HPC-UGent)
 """
@@ -38,22 +40,17 @@
 
 def is_new_existing_path(new_path, paths):
     """
-    Check whether specified path exists and is a new path compared to provided list of paths.
+    Check whether specified path exists and is a new path compared to provided list of paths (that surely exist as they
+    were checked before).
     """
+    if not os.path.exists(new_path):
+        return False
 
-    # assume path is new, until proven otherwise
-    res = True
-
-    if os.path.exists(new_path):
-        for path in paths:
-            if os.path.exists(path) and os.path.samefile(new_path, path):
-                res = False
-                break
-    else:
-        # path doesn't exist
-        res = False
+    for path in paths:
+        if os.path.exists(path) and os.path.samefile(new_path, path):
+            return False
 
-    return res
+    return True
 
 
 cmd = sys.argv[1]
@@ -63,9 +60,9 @@ def is_new_existing_path(new_path, paths):
 
 # determine whether or not to use -Wl to pass options to the linker based on name of command
 if cmd in ['ld', 'ld.gold', 'ld.bfd']:
-    flag_prefix = ''
+    ldflag_prefix = ''
 else:
-    flag_prefix = '-Wl,'
+    ldflag_prefix = '-Wl,'
 
 rpath_filter = rpath_filter.split(',')
 if rpath_filter:
@@ -124,7 +121,7 @@ def is_new_existing_path(new_path, paths):
             if is_new_existing_path(lib_path, rpath_lib_paths):
                 # inject -rpath flag in front for every -L with an absolute path,
                 rpath_lib_paths.append(lib_path)
-                cmd_args_rpath.append(flag_prefix + '-rpath=%s' % lib_path)
+                cmd_args_rpath.append(ldflag_prefix + '-rpath=%s' % lib_path)
 
         # always retain -L flag (without reordering!)
         cmd_args.append('-L%s' % lib_path)
@@ -135,8 +132,12 @@ def is_new_existing_path(new_path, paths):
     # --enable-new-dtags is not removed but replaced to prevent issues when linker flag is forwarded from the compiler
     # to the linker with an extra prefixed flag (either -Xlinker or -Wl,).
     # In that case, the compiler would erroneously pass the next random argument to the linker.
-    elif arg == flag_prefix + '--enable-new-dtags':
-        cmd_args.append(flag_prefix + '--disable-new-dtags')
+    elif arg == '-Xlinker' and args[idx+1] == '--enable-new-dtags':  # detect '-Xlinker --enable-new-dtags'
+        cmd_args.append(ldflag_prefix + '--disable-new-dtags')
+        idx += 1
+    elif arg == ldflag_prefix + '--enable-new-dtags':  # detect '--enable-new-dtags' or '-Wl,--enable-new-dtags'
+        cmd_args.append(ldflag_prefix + '--disable-new-dtags')
+
     else:
         cmd_args.append(arg)
 
@@ -149,14 +150,14 @@ def is_new_existing_path(new_path, paths):
         # avoid using duplicate library paths
         if is_new_existing_path(lib_path, rpath_lib_paths):
             rpath_lib_paths.append(lib_path)
-            cmd_args_rpath.append(flag_prefix + '-rpath=%s' % lib_path)
+            cmd_args_rpath.append(ldflag_prefix + '-rpath=%s' % lib_path)
 
 if add_rpath_args:
     # try to make sure that RUNPATH is not used by always injecting --disable-new-dtags
-    cmd_args_rpath.insert(0, flag_prefix + '--disable-new-dtags')
+    cmd_args_rpath.insert(0, ldflag_prefix + '--disable-new-dtags')
 
     # add -rpath options for paths listed in rpath_include
-    cmd_args_rpath = [flag_prefix + '-rpath=%s' % inc for inc in rpath_include] + cmd_args_rpath
+    cmd_args_rpath = [ldflag_prefix + '-rpath=%s' % inc for inc in rpath_include] + cmd_args_rpath
 
     # add -rpath flags in front
     cmd_args = cmd_args_rpath + cmd_args
@@ -164,5 +165,5 @@ def is_new_existing_path(new_path, paths):
 # wrap all arguments into single quotes to avoid further bash expansion
 cmd_args = ["'%s'" % a.replace("'", "''") for a in cmd_args]
 
-# output: statement to define $CMD_ARGS and $RPATH_ARGS
+# output: statement to define $CMD_ARGS
 print("CMD_ARGS=(%s)" % ' '.join(cmd_args))
diff --git a/test/framework/toolchain.py b/test/framework/toolchain.py
index 6e6910a640..82c7146ce9 100644
--- a/test/framework/toolchain.py
+++ b/test/framework/toolchain.py
@@ -2546,6 +2546,22 @@ def test_rpath_args_script(self):
         ]
         self.assertEqual(res.output.strip(), "CMD_ARGS=(%s)" % ' '.join(cmd_args))
 
+        # compiler command, -Xlinker --enable-new-dtags should be replaced with -Wl,--disable-new-dtags
+        with self.mocked_stdout_stderr():
+            res = run_shell_cmd(f"{script} gcc '' '{rpath_inc}' -Xlinker --enable-new-dtags foo.c")
+        self.assertEqual(res.exit_code, 0)
+        cmd_args = [
+            "'-Wl,-rpath=%s/lib'" % self.test_prefix,
+            "'-Wl,-rpath=%s/lib64'" % self.test_prefix,
+            "'-Wl,-rpath=$ORIGIN'",
+            "'-Wl,-rpath=$ORIGIN/../lib'",
+            "'-Wl,-rpath=$ORIGIN/../lib64'",
+            "'-Wl,--disable-new-dtags'",
+            "'-Wl,--disable-new-dtags'",
+            "'foo.c'",
+        ]
+        self.assertEqual(res.output.strip(), "CMD_ARGS=(%s)" % ' '.join(cmd_args))
+
         # test passing no arguments
         with self.mocked_stdout_stderr():
             res = run_shell_cmd(f"{script} gcc '' '{rpath_inc}'")