diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 14a1a597f..7cbde0c86 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -13,7 +13,7 @@ repos:
           - prettier@3.3.3
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "2.7.3"
+    rev: "3.0.3"
     hooks:
       - id: editorconfig-checker
         alias: ec
diff --git a/nf_core/pipeline-template/.pre-commit-config.yaml b/nf_core/pipeline-template/.pre-commit-config.yaml
index 4dc0f1dcd..9e9f0e1c4 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@3.2.5
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "2.7.3"
+    rev: "3.0.3"
     hooks:
       - id: editorconfig-checker
         alias: ec