diff --git a/.nengobones.yml b/.nengobones.yml
index 99f42494..6846c32d 100644
--- a/.nengobones.yml
+++ b/.nengobones.yml
@@ -184,7 +184,7 @@ docs_conf_py:
     changelog.html: changes.html
 
 pyproject_toml:
-  exclude:
+  black_exclude:
     - tests/ignoreme/ignoreme.py
     - tests/ignoreme/ignoreme.py
 
diff --git a/CHANGES.rst b/CHANGES.rst
index 0ee58d54..4556a37a 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -30,6 +30,8 @@ Release History
   license text will be added to the top of all python files, and ``bones check`` will
   check for the existence of that text. (`#189`_)
 - Added ``gpl-v2`` license type. (`#192`_)
+- Added ``isort_exclude`` option to the ``pyproject_toml`` config, which 
+  can be used by ``isort`` to skip files or directories via regex patterns. (`#196`_)
 
 **Changed**
 
@@ -38,6 +40,10 @@ Release History
 - Tests now default to using the ``worksteal`` xdist option, with 3 workers. (`#186`_)
 - Modified ``check-deploy`` to skip checks when no ``.pypirc`` file present. (`#187`_)
 - Use micromamba to set up python environments. (`#188`_)
+- Changed the ``exclude`` option to ``black_exclude`` in the ``pyproject_toml`` 
+  config. (`#196`_)
+- ``pyproject_toml`` config now sets ``skip_gitignore`` flag to true by default.
+  (`#196`_)
 
 **Removed**
 
@@ -63,6 +69,7 @@ Release History
 .. _#189: https://github.com/nengo/nengo-bones/pull/189
 .. _#191: https://github.com/nengo/nengo-bones/pull/191
 .. _#192: https://github.com/nengo/nengo-bones/pull/192
+.. _#196: https://github.com/nengo/nengo-bones/pull/196
 
 22.11.15 (November 15, 2022)
 ============================
diff --git a/docs/examples/configuration.ipynb b/docs/examples/configuration.ipynb
index f66e1165..490237a9 100644
--- a/docs/examples/configuration.ipynb
+++ b/docs/examples/configuration.ipynb
@@ -1168,12 +1168,16 @@
    "source": [
     "## pyproject.toml config\n",
     "\n",
-    "The only configuration available for this file is an `exclude` option that accepts a\n",
-    "list of patterns to exclude from ``black``. Each entry is a regular expression.\n",
+    "The `pyproject.toml` template has two available configurations:\n",
+    "- ``black_exclude``: A list of patterns to exclude during ``black`` formatting.\n",
+    "- ``isort_exclude``: A list of patterns to exclude during ``isort`` formatting.\n",
+    "\n",
+    "For each configuration option, the entries must be valid regular expressions.\n",
     "\n",
     "When you add this file to your `.nengobones.yml` file, you should also add something\n",
-    "to your documentation to indicate that users should configure their editor to run Black\n",
-    "automatically."
+    "to your documentation to indicate that users should configure their editor to run\n",
+    "``black``\n",
+    "and/or ``isort`` automatically."
    ]
   },
   {
@@ -1184,8 +1188,10 @@
    "source": [
     "nengobones_yml = \"\"\"\n",
     "pyproject_toml:\n",
-    "    exclude:\n",
+    "    black_exclude:\n",
     "        - project/ignore_me.py\n",
+    "    isort_exclude:\n",
+    "        - project/ignore_me/**\n",
     "\"\"\"\n",
     "write_yml(nengobones_yml)\n",
     "\n",
diff --git a/nengo_bones/templates/pyproject.toml.template b/nengo_bones/templates/pyproject.toml.template
index ac72e7c5..4a5c3673 100644
--- a/nengo_bones/templates/pyproject.toml.template
+++ b/nengo_bones/templates/pyproject.toml.template
@@ -8,10 +8,10 @@ requires = ["setuptools<64", "wheel"]
 {% block black %}
 [tool.black]
 target-version = ['py{{ min_python | replace(".", "") }}']
-{% if exclude %}
+{% if black_exclude %}
 force_exclude = '''
 (
-    {% for pattern in exclude %}
+    {% for pattern in black_exclude %}
     {{ "" }}{% if not loop.first %}| {% endif %}{{ pattern }}
     {% endfor %}
 )
@@ -23,6 +23,13 @@ force_exclude = '''
 [tool.isort]
 profile = "black"
 src_paths = ["{{ pkg_name }}"]
+skip_gitignore = true
+{% if isort_exclude %}
+extend_skip_glob = [
+    {% for pattern in isort_exclude %}
+    {{ "" }}{% if not loop.first %}, {% endif %}"{{ pattern }}"
+    {% endfor %}]
+{% endif %}
 {% endblock %}
 
 {% block docformatter %}
diff --git a/nengo_bones/tests/test_generate_bones.py b/nengo_bones/tests/test_generate_bones.py
index 06dea58c..9574f196 100644
--- a/nengo_bones/tests/test_generate_bones.py
+++ b/nengo_bones/tests/test_generate_bones.py
@@ -323,6 +323,46 @@ def test_manifest(tmp_path):
     assert has_line("recursive-exclude *.bak")
 
 
+def test_pyproject_toml(tmp_path):
+    write_nengobones(
+        tmp_path=tmp_path,
+        contents="""
+        pyproject_toml:
+            black_exclude:
+              - this-folder/
+            isort_exclude:
+              - that-folder/**
+        """,
+    )
+
+    result = CliRunner().invoke(
+        bones,
+        [
+            "generate",
+            "--conf-file",
+            str(tmp_path / ".nengobones.yml"),
+            "--output-dir",
+            str(tmp_path),
+            "pyproject-toml",
+        ],
+    )
+    assert_exit(result, 0)
+
+    with (tmp_path / "pyproject.toml").open() as f:
+        lines = f.readlines()
+
+    has_line = make_has_line(lines)
+    assert has_line("# Automatically generated by nengo-bones")
+    assert has_line("force_exclude = '''")
+    assert has_line("(")
+    assert has_line("    this-folder/")
+    assert has_line(")")
+    assert has_line("'''")
+    assert has_line("extend_skip_glob = [")
+    assert has_line('    "that-folder/**"')
+    assert has_line("]")
+
+
 def test_setup_py(tmp_path):
     write_nengobones(
         tmp_path=tmp_path,
diff --git a/nengo_bones/version.py b/nengo_bones/version.py
index 823d13c9..061efa50 100644
--- a/nengo_bones/version.py
+++ b/nengo_bones/version.py
@@ -11,7 +11,7 @@
 tagged with the version.
 """
 
-version_info = (24, 1, 15)  # bones: ignore
+version_info = (24, 1, 22)  # bones: ignore
 
 name = "nengo-bones"
 dev = 0
diff --git a/pyproject.toml b/pyproject.toml
index 00e69521..6c0a8b51 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,6 +15,7 @@ force_exclude = '''
 [tool.isort]
 profile = "black"
 src_paths = ["nengo_bones"]
+skip_gitignore = true
 
 [tool.docformatter]
 wrap-summaries = 88