diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index a22aa24b4..6fe64e4e2 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -13,7 +13,7 @@ repos:
           - prettier@3.5.0
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "3.1.2"
+    rev: "3.2.0"
     hooks:
       - id: editorconfig-checker
         alias: ec
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 590965907..9459b0bc1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -24,6 +24,7 @@
 - chore(deps): update python:3.12-slim docker digest to 69ce3ae ([#3433](https://github.com/nf-core/tools/pull/3433))
 - chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.9.4 ([#3438](https://github.com/nf-core/tools/pull/3438))
 - format name/value with YAML syntax ([#3442](https://github.com/nf-core/tools/pull/3442))
+- chore(deps): update pre-commit hook editorconfig-checker/editorconfig-checker.python to v3.2.0 ([#3446](https://github.com/nf-core/tools/pull/3446))
 - chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.9.5 ([#3445](https://github.com/nf-core/tools/pull/3445))
 - chore(deps): update pre-commit hook pre-commit/mirrors-mypy to v1.15.0 ([#3447](https://github.com/nf-core/tools/pull/3447))
 - Update prettier to 3.5.0 ([#3448](https://github.com/nf-core/tools/pull/3448))
diff --git a/nf_core/pipeline-template/.pre-commit-config.yaml b/nf_core/pipeline-template/.pre-commit-config.yaml
index 0ad2aa575..f034bfbba 100644
--- a/nf_core/pipeline-template/.pre-commit-config.yaml
+++ b/nf_core/pipeline-template/.pre-commit-config.yaml
@@ -7,7 +7,7 @@ repos:
           - prettier@3.5.0
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "3.1.2"
+    rev: "3.2.0"
     hooks:
       - id: editorconfig-checker
         alias: ec