diff --git a/CHANGELOG.md b/CHANGELOG.md
index 577c8ed101..96a41dcb00 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -41,6 +41,7 @@
 - Update gitpod/workspace-base Docker digest to 77021d8 ([#3649](https://github.com/nf-core/tools/pull/3649))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.12.1 ([#3648](https://github.com/nf-core/tools/pull/3648))
 - Update error message for rocrate_readme_sync ([#3652](https://github.com/nf-core/tools/pull/3652))
+- Fix collectFile cache issue causing software version inconsistencies ([#3654](https://github.com/nf-core/tools/pull/3654))
 
 ## [v3.3.1 - Tungsten Tamarin Patch](https://github.com/nf-core/tools/releases/tag/3.3.1) - [2025-06-02]
 
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
index 6126f9ec69..06c7f58cd9 100644
--- a/nf_core/pipeline-template/workflows/pipeline.nf
+++ b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -55,7 +55,8 @@ workflow {{ short_name|upper }} {
             storeDir: "${params.outdir}/pipeline_info",
             name: {% if is_nfcore %}'nf_core_'  + {% endif %} '{{ short_name }}_software_' {% if multiqc %} + 'mqc_' {% endif %} + 'versions.yml',
             sort: true,
-            newLine: true
+            newLine: true,
+            cache: false
         ).set { ch_collated_versions }
 
 {% if multiqc %}