diff --git a/CHANGELOG.md b/CHANGELOG.md
index 70b606932b..16573a91e2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -16,6 +16,7 @@
 
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.4 ([#2974](https://github.com/nf-core/tools/pull/2974))
 - Update gitpod/workspace-base Docker digest to 92dd1bc ([#2982](https://github.com/nf-core/tools/pull/2982))
+- Update output of generation script for API docs to new structure ([#2988](https://github.com/nf-core/tools/pull/2988))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 
diff --git a/docs/api/generate-api-docs.sh b/docs/api/generate-api-docs.sh
index 6b3c3abfa3..f2b905c0c3 100644
--- a/docs/api/generate-api-docs.sh
+++ b/docs/api/generate-api-docs.sh
@@ -28,7 +28,7 @@ done
 
 # Set the output directory if not set
 if [[ -z "$output_dir" ]]; then
-    output_dir="../src/content/tools/docs"
+    output_dir="../src/content/api_reference"
 fi
 
 # if no release is specified, use all releases