diff --git a/easybuild/tools/options.py b/easybuild/tools/options.py
index fe2abe75f7..8a95aa7226 100644
--- a/easybuild/tools/options.py
+++ b/easybuild/tools/options.py
@@ -123,7 +123,7 @@ def terminal_supports_colors(stream):
 CONFIG_ENV_VAR_PREFIX = 'EASYBUILD'
 
 XDG_CONFIG_HOME = os.environ.get('XDG_CONFIG_HOME', os.path.join(os.path.expanduser('~'), ".config"))
-XDG_CONFIG_DIRS = os.environ.get('XDG_CONFIG_DIRS', '/etc').split(os.pathsep)
+XDG_CONFIG_DIRS = os.environ.get('XDG_CONFIG_DIRS', '/etc/xdg').split(os.pathsep)
 DEFAULT_SYS_CFGFILES = [f for d in XDG_CONFIG_DIRS for f in sorted(glob.glob(os.path.join(d, 'easybuild.d', '*.cfg')))]
 DEFAULT_USER_CFGFILE = os.path.join(XDG_CONFIG_HOME, 'easybuild', 'config.cfg')
 
@@ -213,6 +213,12 @@ class EasyBuildOptions(GeneralOption):
 
     DEFAULT_LOGLEVEL = 'INFO'
     DEFAULT_CONFIGFILES = DEFAULT_SYS_CFGFILES[:]
+    if 'XDG_CONFIG_DIRS' not in os.environ:
+        old_etc_location = os.path.join('/etc', 'easybuild.d')
+        if os.path.isdir(old_etc_location) and glob.glob(os.path.join(old_etc_location, '*.cfg')):
+            _log.deprecated(f"Using {old_etc_location} is deprecated. Please use "
+                            "/etc/xdg/easybuild.d instead or add /etc to XDG_CONFIG_DIRS", '6.0')
+
     if os.path.exists(DEFAULT_USER_CFGFILE):
         DEFAULT_CONFIGFILES.append(DEFAULT_USER_CFGFILE)
 
@@ -1322,7 +1328,7 @@ def show_default_configfiles(self):
             '',
             "* user-level: %s" % os.path.join('${XDG_CONFIG_HOME:-$HOME/.config}', 'easybuild', 'config.cfg'),
             "  -> %s => %s" % (DEFAULT_USER_CFGFILE, ('not found', 'found')[os.path.exists(DEFAULT_USER_CFGFILE)]),
-            "* system-level: %s" % os.path.join('${XDG_CONFIG_DIRS:-/etc}', 'easybuild.d', '*.cfg'),
+            "* system-level: %s" % os.path.join('${XDG_CONFIG_DIRS:-/etc/xdg}', 'easybuild.d', '*.cfg'),
             "  -> %s => %s" % (system_cfg_glob_paths, ', '.join(DEFAULT_SYS_CFGFILES) or "(no matches)"),
             '',
             "Default list of existing configuration files (%d): %s" % (found_cfgfile_cnt, found_cfgfile_list),
diff --git a/test/framework/options.py b/test/framework/options.py
index 089b068e62..6e7823f907 100644
--- a/test/framework/options.py
+++ b/test/framework/options.py
@@ -3497,7 +3497,7 @@ def test_show_default_configfiles(self):
             '',
             "* user-level: ${XDG_CONFIG_HOME:-$HOME/.config}/easybuild/config.cfg",
             "  -> %s",
-            "* system-level: ${XDG_CONFIG_DIRS:-/etc}/easybuild.d/*.cfg",
+            "* system-level: ${XDG_CONFIG_DIRS:-/etc/xdg}/easybuild.d/*.cfg",
             "  -> %s/easybuild.d/*.cfg => ",
         ])
 
@@ -3512,12 +3512,12 @@ def test_show_default_configfiles(self):
             homecfgfile_str += " => found"
         else:
             homecfgfile_str += " => not found"
-        expected = expected_tmpl % ('(not set)', '(not set)', homecfgfile_str, '{/etc}')
+        expected = expected_tmpl % ('(not set)', '(not set)', homecfgfile_str, '{/etc/xdg}')
         self.assertIn(expected, logtxt)
 
         # to predict the full output, we need to take control over $HOME and $XDG_CONFIG_DIRS
         os.environ['HOME'] = self.test_prefix
-        xdg_config_dirs = os.path.join(self.test_prefix, 'etc')
+        xdg_config_dirs = os.path.join(self.test_prefix, 'etc', 'xdg')
         os.environ['XDG_CONFIG_DIRS'] = xdg_config_dirs
 
         expected_tmpl += '\n'.join([
@@ -3542,12 +3542,12 @@ def test_show_default_configfiles(self):
 
         xdg_config_home = os.path.join(self.test_prefix, 'home')
         os.environ['XDG_CONFIG_HOME'] = xdg_config_home
-        xdg_config_dirs = [os.path.join(self.test_prefix, 'etc'), os.path.join(self.test_prefix, 'moaretc')]
+        xdg_config_dirs = [os.path.join(self.test_prefix, 'etc', 'xdg'), os.path.join(self.test_prefix, 'moaretc')]
         os.environ['XDG_CONFIG_DIRS'] = os.pathsep.join(xdg_config_dirs)
 
         # put various dummy cfgfiles in place
         cfgfiles = [
-            os.path.join(self.test_prefix, 'etc', 'easybuild.d', 'config.cfg'),
+            os.path.join(self.test_prefix, 'etc', 'xdg', 'easybuild.d', 'config.cfg'),
             os.path.join(self.test_prefix, 'moaretc', 'easybuild.d', 'bar.cfg'),
             os.path.join(self.test_prefix, 'moaretc', 'easybuild.d', 'foo.cfg'),
             os.path.join(xdg_config_home, 'easybuild', 'config.cfg'),