diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index d1b83ce3f..6aa89cbe5 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -66,8 +66,10 @@ params {
     validate_params            = true
 
 }
+{% if modules %}
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
+{% endif %}
 {% if nf_core_configs -%}
 // Load nf-core custom profiles from different Institutions
 try {
diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml
index 8d8186f32..40f25e397 100644
--- a/nf_core/pipelines/create/templatefeatures.yml
+++ b/nf_core/pipelines/create/templatefeatures.yml
@@ -244,6 +244,7 @@ fastqc:
   custom_pipelines: True
 modules:
   skippable_paths:
+    - "conf/base.config"
     - "conf/modules.config"
     - "modules.json"
     - "modules"
@@ -259,6 +260,7 @@ modules:
     base_config: False
     modules_config: False
     files_exist:
+      - "conf/base.config"
       - "conf/modules.config"
       - "modules.json"
     nextflow_config: