diff --git a/nf_core/lint/params_used.py b/nf_core/lint/params_used.py
index e58bf04be3..046d20221b 100644
--- a/nf_core/lint/params_used.py
+++ b/nf_core/lint/params_used.py
@@ -1,6 +1,9 @@
 #!/usr/bin/env python
 
 import os
+import logging
+
+log = logging.getLogger(__name__)
 
 
 def params_used(self):
@@ -28,6 +31,9 @@ def params_used(self):
         if cf in ignore_params:
             ignored.append("Config variable ignored: {}".format(self._wrap_quotes(cf)))
             continue
+        if cf.count(".") > 1:
+            log.debug(f"Ignoring nested param: {cf}")
+            continue
         if cf in main_nf:
             passed.append("Config variable found in `main.nf`: {}".format(self._wrap_quotes(cf)))
         else: