diff --git a/CHANGELOG.md b/CHANGELOG.md
index 08786347fa..a37e6e5ff7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,7 @@
 - Add empty line in README.md to fix badges. ([#2729](https://github.com/nf-core/tools/pull/2729))
 - Replace automatic branch detection in `nf-core download` CI test with hardcoded `dev` and input. ([#2727](https://github.com/nf-core/tools/pull/2727))
 - Add Github Action to automatically cleanup ubuntu-latest runners to fix runner running out of diskspace errors([#2755](https://github.com/nf-core/tools/issues/2755))
+- Fix GitHub Actions CI and Linting badges links ([#2757](https://github.com/nf-core/tools/pull/2757))
 
 ### Linting
 
diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md
index 1c4c34cd41..037d3fd81a 100644
--- a/nf_core/pipeline-template/README.md
+++ b/nf_core/pipeline-template/README.md
@@ -9,8 +9,8 @@
 
 {% endif -%}
 {% if github_badges -%}
-[![GitHub Actions CI Status](https://github.com/{{ name }}/workflows/nf-core%20CI/badge.svg)](https://github.com/{{ name }}/actions?query=workflow%3A%22nf-core+CI%22)
-[![GitHub Actions Linting Status](https://github.com/{{ name }}/workflows/nf-core%20linting/badge.svg)](https://github.com/{{ name }}/actions?query=workflow%3A%22nf-core+linting%22){% endif -%}
+[![GitHub Actions CI Status](https://github.com/{{ name }}/actions/workflows/ci.yml/badge.svg)](https://github.com/{{ name }}/actions/workflows/ci.yml)
+[![GitHub Actions Linting Status](https://github.com/{{ name }}/actions/workflows/linting.yml/badge.svg)](https://github.com/{{ name }}/actions/workflows/linting.yml){% endif -%}
 {% if branded -%}[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/{{ short_name }}/results){% endif -%}
 {%- if github_badges -%}
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)