diff --git a/scripts/pyproject.toml b/scripts/pyproject.toml
index 3e115d52..fe080f05 100644
--- a/scripts/pyproject.toml
+++ b/scripts/pyproject.toml
@@ -61,6 +61,11 @@ filterwarnings = ["error"]
 
 [tool.ruff]
 line-length = 120
+
+[tool.ruff.format]
+docstring-code-format = true
+
+[tool.ruff.lint]
 allowed-confusables = ["’", "×"]
 select = [
     "A",
@@ -96,13 +101,10 @@ ignore = [
 ]
 unfixable = ["RUF001"]  # never “fix” “confusables”
 
-[tool.ruff.format]
-docstring-code-format = true
-
-[tool.ruff.isort]
+[tool.ruff.lint.isort]
 known-first-party = ["scverse_template_scripts"]
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "tests/*.py" = [
     "ARG001",  # pytest fixtures don’t need to be used
     "PLR0913",  # allow as many pytest fixtures being used as one likes
diff --git a/{{cookiecutter.project_name}}/pyproject.toml b/{{cookiecutter.project_name}}/pyproject.toml
index 71ac7557..ff5f9f61 100644
--- a/{{cookiecutter.project_name}}/pyproject.toml
+++ b/{{cookiecutter.project_name}}/pyproject.toml
@@ -68,8 +68,14 @@ addopts = [
 ]
 
 [tool.ruff]
-src = ["src"]
 line-length = 120
+src = ["src"]
+extend-include = ["*.ipynb"]
+
+[tool.ruff.format]
+docstring-code-format = true
+
+[tool.ruff.lint]
 select = [
     "F",  # Errors detected by Pyflakes
     "E",  # Error detected by Pycodestyle
@@ -110,15 +116,11 @@ ignore = [
     # We want docstrings to start immediately after the opening triple quote
     "D213",
 ]
-extend-include = ["*.ipynb"]
-
-[tool.ruff.format]
-docstring-code-format = true
 
-[tool.ruff.pydocstyle]
+[tool.ruff.lint.pydocstyle]
 convention = "numpy"
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "docs/*" = ["I"]
 "tests/*" = ["D"]
 "*/__init__.py" = ["F401"]