diff --git a/CHANGELOG.md b/CHANGELOG.md
index 30bd00b5c..6a11aee51 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -38,6 +38,7 @@
 - add option to exclude tower.yml from pipeline template ([#3134](https://github.com/nf-core/tools/pull/3134))
 - run nf-core lint `--release` on PRs to master ([#3148](https://github.com/nf-core/tools/pull/3148))
 - Add tests to ensure all files are part of a template customisation group and all groups are tested ([#3099](https://github.com/nf-core/tools/pull/3099))
+- Remove if/else block to include `igenomes.config` ([#3168](https://github.com/nf-core/tools/pull/3168))
 - Replaces the old custom `check_max()` function with the Nextflow native `resourceLimits` directive ([#3037](https://github.com/nf-core/tools/pull/3037))
 - Fixed release announcement hashtags for Mastodon ([#3099](https://github.com/nf-core/tools/pull/3176))
 
diff --git a/nf_core/pipeline-template/conf/igenomes_ignored.config b/nf_core/pipeline-template/conf/igenomes_ignored.config
new file mode 100644
index 000000000..b4034d824
--- /dev/null
+++ b/nf_core/pipeline-template/conf/igenomes_ignored.config
@@ -0,0 +1,9 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for iGenomes paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Empty genomes dictionary to use when igenomes is ignored.
+----------------------------------------------------------------------------------------
+*/
+
+params.genomes = [:]
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index cc82d1c1c..39c352136 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -211,11 +211,7 @@ charliecloud.registry = 'quay.io'
 
 {% if igenomes -%}
 // Load igenomes.config if required
-if (!params.igenomes_ignore) {
-    includeConfig 'conf/igenomes.config'
-} else {
-    params.genomes = [:]
-}
+includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'
 {% endif -%}
 
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container
diff --git a/nf_core/pipelines/create/template_features.yml b/nf_core/pipelines/create/template_features.yml
index b59a2e51a..6f476cdfb 100644
--- a/nf_core/pipelines/create/template_features.yml
+++ b/nf_core/pipelines/create/template_features.yml
@@ -60,6 +60,7 @@ ci:
 igenomes:
   skippable_paths:
     - "conf/igenomes.config"
+    - "conf/igenomes_ignored.config"
   short_description: "Use reference genomes"
   description: "The pipeline will be configured to use a copy of the most common reference genome files from iGenomes"
   help_text: |
@@ -76,6 +77,7 @@ igenomes:
   linting:
     files_exist:
       - "conf/igenomes.config"
+      - "conf/igenomes_ignored.config"
   nfcore_pipelines: True
   custom_pipelines: True
 github_badges:
diff --git a/nf_core/pipelines/lint/files_exist.py b/nf_core/pipelines/lint/files_exist.py
index bd25ff33d..9dd307d8b 100644
--- a/nf_core/pipelines/lint/files_exist.py
+++ b/nf_core/pipelines/lint/files_exist.py
@@ -167,6 +167,7 @@ def files_exist(self) -> Dict[str, List[str]]:
         [Path("assets", "multiqc_config.yml")],
         [Path("conf", "base.config")],
         [Path("conf", "igenomes.config")],
+        [Path("conf", "igenomes_ignored.config")],
         [Path(".github", "workflows", "awstest.yml")],
         [Path(".github", "workflows", "awsfulltest.yml")],
         [Path("modules.json")],