diff --git a/reframe/core/pipeline.py b/reframe/core/pipeline.py
index 77901f62a..b43b94318 100644
--- a/reframe/core/pipeline.py
+++ b/reframe/core/pipeline.py
@@ -465,7 +465,8 @@ def resolve_external_references(self, test):
                 raise ReferenceParseError(f'{self.__ref_file}: {err}') from err
 
     def _read_ref_file(self, filename):
-        def _parse_ref_entry(key, val):
+        def _parse_ref_entry(key_path, val):
+            key = '.'.join(str(k) for k in key_path)
             try:
                 first = val[0]
             except (TypeError, IndexError):
@@ -483,17 +484,17 @@ def _parse_ref_entry(key, val):
             else:
                 return tuple(val)
 
-        def _entry(key, val, full_key, max_depth):
-            level = len(full_key.split('.')) - 2
+        def _entry(key, val, key_path, max_depth):
+            level = len(key_path) - 2
             if level == 0 and key == '$index':
                 return tuple(val)
 
             if level < max_depth and isinstance(val, dict):
-                return {k: _entry(k, v, f'{full_key}.{k}', max_depth)
+                return {k: _entry(k, v, key_path + [k], max_depth)
                         for k, v in val.items()}
 
             if level == max_depth:
-                return _parse_ref_entry(full_key, val)
+                return _parse_ref_entry(key_path, val)
 
             return val
 
@@ -518,7 +519,7 @@ def _entry(key, val, full_key, max_depth):
 
         for key, val in ref_yaml.items():
             mkref[key] = _entry(
-                key, val, f'{self.__test_entry_name}.{key}', max_level
+                key, val, [self.__test_entry_name, key], max_level
             )
 
         return mkref
diff --git a/unittests/test_pipeline.py b/unittests/test_pipeline.py
index 78d03aeb4..391d4a515 100644
--- a/unittests/test_pipeline.py
+++ b/unittests/test_pipeline.py
@@ -1971,7 +1971,8 @@ def test_reference_external_with_index(make_perftest, make_path,
         'MyTest': {
             '$index': ['$processor.arch', '$dev.gpu.model'],
             'skylake': {
-                'p100': {
+                # We use a regex here to check also regexes in external files
+                'p100.*': {
                     'value1': [1.4, -0.1, 0.1, None],
                     'value2': [1.7, -0.1, 0.1, None],
                     'value3': [3.1, -0.1, 0.1, None]