diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8c13e54f7..7f7ce2ea6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,7 @@
 
 - Fixed an issue where the linting CI action didn't read the correct file ([#3202](https://github.com/nf-core/tools/pull/3202))
 - Fixed condition for `awsfulltest` to run ([#3203](https://github.com/nf-core/tools/pull/3203))
+- Fix too many empty lines added to .editorconfig file ([#3204](https://github.com/nf-core/tools/pull/3204))
 
 ## [v3.0.0 - Titanium Tapir](https://github.com/nf-core/tools/releases/tag/3.0.0) - [2024-10-08]
 
diff --git a/nf_core/pipeline-template/.editorconfig b/nf_core/pipeline-template/.editorconfig
index 1db986f5b..c78ec8e96 100644
--- a/nf_core/pipeline-template/.editorconfig
+++ b/nf_core/pipeline-template/.editorconfig
@@ -11,7 +11,7 @@ indent_style = space
 [*.{md,yml,yaml,html,css,scss,js}]
 indent_size = 2
 
-{% if modules %}
+{% if modules -%}
 # These files are edited and tested upstream in nf-core/modules
 [/modules/nf-core/**]
 charset = unset
@@ -25,12 +25,12 @@ end_of_line = unset
 insert_final_newline = unset
 trim_trailing_whitespace = unset
 indent_style = unset
-{% endif %}
+{%- endif %}
 
-{% if email %}
+{% if email -%}
 [/assets/email*]
 indent_size = unset
-{% endif %}
+{%- endif %}
 
 # ignore python and markdown
 [*.{py,md}]