diff --git a/CHANGELOG.md b/CHANGELOG.md
index ca7dce23b2..20f48bb1ce 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -49,6 +49,7 @@
 - Update GitHub Actions ([#3237](https://github.com/nf-core/tools/pull/3237))
 - add `--dir/-d` option to schema commands ([#3247](https://github.com/nf-core/tools/pull/3247))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.1 ([#3250](https://github.com/nf-core/tools/pull/3250))
+- fix headers in api docs ([#3323](https://github.com/nf-core/tools/pull/3323))
 - handle new schema structure in `nf-core pipelines create-params-file` ([#3276](https://github.com/nf-core/tools/pull/3276))
 - Update Gitpod image to use Miniforge instead of Miniconda([#3274](https://github.com/nf-core/tools/pull/3274))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.3 ([#3275](https://github.com/nf-core/tools/pull/3275))
diff --git a/docs/api/_src/api/pipelines/bump_version.md b/docs/api/_src/api/pipelines/bump_version.md
index cd7dc280f6..76db67837a 100644
--- a/docs/api/_src/api/pipelines/bump_version.md
+++ b/docs/api/_src/api/pipelines/bump_version.md
@@ -1,4 +1,4 @@
-# nf_core.bump_version
+# nf_core.pipelines.bump_version
 
 ```{eval-rst}
 .. automodule:: nf_core.pipelines.bump_version
diff --git a/docs/api/_src/api/pipelines/create.md b/docs/api/_src/api/pipelines/create.md
index 576335e951..5019a5f3c8 100644
--- a/docs/api/_src/api/pipelines/create.md
+++ b/docs/api/_src/api/pipelines/create.md
@@ -1,4 +1,4 @@
-# nf_core.create
+# nf_core.pipelines.create
 
 ```{eval-rst}
 .. automodule:: nf_core.pipelines.create
diff --git a/docs/api/_src/api/pipelines/download.md b/docs/api/_src/api/pipelines/download.md
index 540fb92c49..afb31ddea6 100644
--- a/docs/api/_src/api/pipelines/download.md
+++ b/docs/api/_src/api/pipelines/download.md
@@ -1,4 +1,4 @@
-# nf_core.download
+# nf_core.pipelines.download
 
 ```{eval-rst}
 .. automodule:: nf_core.pipelines.download
diff --git a/docs/api/_src/api/pipelines/launch.md b/docs/api/_src/api/pipelines/launch.md
index 0f7fc03f64..0d0260cae6 100644
--- a/docs/api/_src/api/pipelines/launch.md
+++ b/docs/api/_src/api/pipelines/launch.md
@@ -1,4 +1,4 @@
-# nf_core.launch
+# nf_core.pipelines.launch
 
 ```{eval-rst}
 .. automodule:: nf_core.pipelines.launch
diff --git a/docs/api/_src/api/pipelines/lint.md b/docs/api/_src/api/pipelines/lint.md
index aa62c404b8..91b37c26f6 100644
--- a/docs/api/_src/api/pipelines/lint.md
+++ b/docs/api/_src/api/pipelines/lint.md
@@ -1,4 +1,4 @@
-# nf_core.lint
+# nf_core.pipelines.lint
 
 :::{seealso}
 See the [Lint Tests](/docs/nf-core-tools/api_reference/dev/pipeline_lint_tests) docs for information about specific linting functions.
diff --git a/docs/api/_src/api/pipelines/list.md b/docs/api/_src/api/pipelines/list.md
index 7df7564544..5f404b91c3 100644
--- a/docs/api/_src/api/pipelines/list.md
+++ b/docs/api/_src/api/pipelines/list.md
@@ -1,4 +1,4 @@
-# nf_core.list
+# nf_core.pipelines.list
 
 ```{eval-rst}
 .. automodule:: nf_core.pipelines.list
diff --git a/docs/api/_src/api/pipelines/params-file.md b/docs/api/_src/api/pipelines/params-file.md
index 06f27cc592..37e91f458a 100644
--- a/docs/api/_src/api/pipelines/params-file.md
+++ b/docs/api/_src/api/pipelines/params-file.md
@@ -1,4 +1,4 @@
-# nf_core.params_file
+# nf_core.pipelines.params_file
 
 ```{eval-rst}
 .. automodule:: nf_core.pipelines.params_file
diff --git a/docs/api/_src/api/pipelines/schema.md b/docs/api/_src/api/pipelines/schema.md
index c885d9ed23..4ca1aab480 100644
--- a/docs/api/_src/api/pipelines/schema.md
+++ b/docs/api/_src/api/pipelines/schema.md
@@ -1,4 +1,4 @@
-# nf_core.schema
+# nf_core.pipelines.schema
 
 ```{eval-rst}
 .. automodule:: nf_core.pipelines.schema
diff --git a/docs/api/_src/api/pipelines/sync.md b/docs/api/_src/api/pipelines/sync.md
index da1f468fe5..f78733bb7d 100644
--- a/docs/api/_src/api/pipelines/sync.md
+++ b/docs/api/_src/api/pipelines/sync.md
@@ -1,4 +1,4 @@
-# nf_core.sync
+# nf_core.pipelines.sync
 
 ```{eval-rst}
 .. automodule:: nf_core.pipelines.sync
diff --git a/docs/api/_src/api/pipelines/utils.md b/docs/api/_src/api/pipelines/utils.md
index 86b8c3f36f..36c2ecca4d 100644
--- a/docs/api/_src/api/pipelines/utils.md
+++ b/docs/api/_src/api/pipelines/utils.md
@@ -1,4 +1,4 @@
-# nf_core.utils
+# nf_core.pipelines.utils
 
 ```{eval-rst}
 .. automodule:: nf_core.pipelines.utils