diff --git a/CHANGELOG.md b/CHANGELOG.md
index bacef3b106..9c9af42a9a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,8 @@
 
 ### Modules
 
+- fix including modules.config ([#3356](https://github.com/nf-core/tools/pull/3356))
+
 ### Subworkflows
 
 ### General
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 36018b1062..9db8f3bfe6 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -77,11 +77,6 @@ params {
 includeConfig 'conf/base.config'
 {%- else %}
 
-{% if modules -%}
-// Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'
-{%- endif %}
-
 process {
     // TODO nf-core: Check the defaults for all processes
     cpus   = { 1    * task.attempt }
@@ -336,3 +331,8 @@ validation {
     }{% endif %}
 }
 {%- endif %}
+
+{% if modules -%}
+// Load modules.config for DSL2 module specific options
+includeConfig 'conf/modules.config'
+{%- endif %}