diff --git a/sdks/python/apache_beam/examples/complete/juliaset/juliaset_main.py b/sdks/python/apache_beam/examples/complete/juliaset/juliaset_main.py
index fb64c2702fd2..110b99b31b5f 100644
--- a/sdks/python/apache_beam/examples/complete/juliaset/juliaset_main.py
+++ b/sdks/python/apache_beam/examples/complete/juliaset/juliaset_main.py
@@ -33,7 +33,13 @@
 startup, will install the tarball.
 
 Below is a complete command line for running the juliaset workflow remotely as
-an example:
+an example.
+
+First, install the juliaset package in the submission environment:
+
+pip install -e .
+
+Then, launch a Beam job:
 
 python juliaset_main.py \
   --job_name juliaset-$USER \
@@ -52,7 +58,7 @@
 
 import logging
 
-from apache_beam.examples.complete.juliaset.juliaset import juliaset
+from juliaset import juliaset
 
 if __name__ == '__main__':
   logging.getLogger().setLevel(logging.INFO)
diff --git a/sdks/python/apache_beam/examples/complete/juliaset/pyproject.toml b/sdks/python/apache_beam/examples/complete/juliaset/pyproject.toml
index 6c865974cbd2..436607838870 100644
--- a/sdks/python/apache_beam/examples/complete/juliaset/pyproject.toml
+++ b/sdks/python/apache_beam/examples/complete/juliaset/pyproject.toml
@@ -27,7 +27,3 @@ description = "Julia set workflow package."
 dependencies = [
   "numpy"
 ]
-
-[build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
diff --git a/sdks/python/apache_beam/examples/complete/juliaset/setup.py b/sdks/python/apache_beam/examples/complete/juliaset/setup.py
index 649a5be7db75..d47cade92d72 100644
--- a/sdks/python/apache_beam/examples/complete/juliaset/setup.py
+++ b/sdks/python/apache_beam/examples/complete/juliaset/setup.py
@@ -14,105 +14,13 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+"""An optional setuptools configuration stub for the pipeline package.
 
-"""setup.py module for the pipeline package.
-
-In this example, the pipeline code is gathered in a package that can be built
-as source distribution and installed on the workers. The package is defined
-in the pyproject.toml file. You can use setup.py file for defining 
-configuration that needs to be determined programatically, for example,
-custom commands to run when a package is installed.
-
-You can install this package into the workers at runtime by using
-the --setup_file pipeline option.
+Use pyproject.toml to define the package. Add this file if you must
+use the --setup_file pipeline option on Beam 2.59.0 or earlier, or
+if your package requires some programmatic configuration at build or
+installation time.
 """
 
-# pytype: skip-file
-
-import subprocess
-
 import setuptools
-
-# It is recommended to import setuptools prior to importing distutils to avoid
-# using legacy behavior from distutils.
-# https://setuptools.readthedocs.io/en/latest/history.html#v48-0-0
-from distutils.command.build import build as _build  # isort:skip
-
-
-# This class handles the pip install mechanism.
-class build(_build):  # pylint: disable=invalid-name
-  """A build command class that will be invoked during package install.
-
-  The package built using the current setup.py will be staged and later
-  installed in the worker using `pip install package'. This class will be
-  instantiated during install for this specific scenario and will trigger
-  running the custom commands specified.
-  """
-  sub_commands = _build.sub_commands + [('CustomCommands', None)]
-
-
-# Some custom command to run during setup. The command is not essential for this
-# workflow. It is used here as an example. Each command will spawn a child
-# process. Typically, these commands will include steps to install non-Python
-# packages. For instance, to install a C++-based library libjpeg62 the following
-# two commands will have to be added:
-#
-#     ['apt-get', 'update'],
-#     ['apt-get', '--assume-yes', 'install', 'libjpeg62'],
-#
-# First, note that there is no need to use the sudo command because the setup
-# script runs with appropriate access.
-# Second, if apt-get tool is used then the first command needs to be 'apt-get
-# update' so the tool refreshes itself and initializes links to download
-# repositories.  Without this initial step the other apt-get install commands
-# will fail with package not found errors. Note also --assume-yes option which
-# shortcuts the interactive confirmation.
-#
-# Note that in this example custom commands will run after installing required
-# packages. If you have a PyPI package that depends on one of the custom
-# commands, move installation of the dependent package to the list of custom
-# commands, e.g.:
-#
-#     ['pip', 'install', 'my_package'],
-#
-# TODO(https://github.com/apache/beam/issues/18568): Output from the custom
-# commands are missing from the logs. The output of custom commands (including
-# failures) will be logged in the worker-startup log.
-CUSTOM_COMMANDS = [['echo', 'Custom command worked!']]
-
-
-class CustomCommands(setuptools.Command):
-  """A setuptools Command class able to run arbitrary commands."""
-  def initialize_options(self):
-    pass
-
-  def finalize_options(self):
-    pass
-
-  def RunCustomCommand(self, command_list):
-    print('Running command: %s' % command_list)
-    p = subprocess.Popen(
-        command_list,
-        stdin=subprocess.PIPE,
-        stdout=subprocess.PIPE,
-        stderr=subprocess.STDOUT)
-    # Can use communicate(input='y\n'.encode()) if the command run requires
-    # some confirmation.
-    stdout_data, _ = p.communicate()
-    print('Command output: %s' % stdout_data)
-    if p.returncode != 0:
-      raise RuntimeError(
-          'Command %s failed: exit code: %s' % (command_list, p.returncode))
-
-  def run(self):
-    for command in CUSTOM_COMMANDS:
-      self.RunCustomCommand(command)
-
-
-setuptools.setup(
-    packages=setuptools.find_packages(),
-    cmdclass={
-        # Command class instantiated and run during pip install scenarios.
-        'build': build,
-        'CustomCommands': CustomCommands,
-    })
+setuptools.setup()
diff --git a/sdks/python/apache_beam/examples/complete/juliaset/src/juliaset/juliaset_test_it.py b/sdks/python/apache_beam/examples/complete/juliaset/src/juliaset/juliaset_test_it.py
index 0aac9f9cffb9..de4f8e9408c2 100644
--- a/sdks/python/apache_beam/examples/complete/juliaset/src/juliaset/juliaset_test_it.py
+++ b/sdks/python/apache_beam/examples/complete/juliaset/src/juliaset/juliaset_test_it.py
@@ -48,7 +48,7 @@ def test_run_example_with_setup_file(self):
         'coordinate_output': coordinate_output,
         'grid_size': self.GRID_SIZE,
         'setup_file': os.path.normpath(
-            os.path.join(os.path.dirname(__file__), '..', 'setup.py')),
+            os.path.join(os.path.dirname(__file__), '../..', 'setup.py')),
         'on_success_matcher': all_of(PipelineStateMatcher(PipelineState.DONE)),
     }
     args = pipeline.get_full_options_as_args(**extra_args)
diff --git a/sdks/python/apache_beam/options/pipeline_options.py b/sdks/python/apache_beam/options/pipeline_options.py
index 0f8457a40a7b..41be865f2354 100644
--- a/sdks/python/apache_beam/options/pipeline_options.py
+++ b/sdks/python/apache_beam/options/pipeline_options.py
@@ -1392,14 +1392,16 @@ def _add_argparse_args(cls, parser):
         '--setup_file',
         default=None,
         help=(
-            'Path to a setup Python file containing package dependencies. If '
-            'specified, the file\'s containing folder is assumed to have the '
-            'structure required for a setuptools setup package. The file must '
-            'be named setup.py. More details: '
-            'https://pythonhosted.org/an_example_pypi_project/setuptools.html '
-            'During job submission a source distribution will be built and '
-            'the worker will install the resulting package before running any '
-            'custom code.'))
+            'Path to a file in that defines a Python package that needs to be '
+            'installed on Beam workers. '
+            'If specified, the file\'s containing folder must have the '
+            'structure required for a Python package. The file must '
+            'be named setup.py or pyproject.toml. '
+            'For information on distributing Python packages, see: '
+            'https://packaging.python.org/ '
+            'During job submission a source distribution of the package will '
+            'be built and workers will install the resulting package before '
+            'running the pipeline.'))
     parser.add_argument(
         '--beam_plugin',
         '--beam_plugins',
diff --git a/sdks/python/apache_beam/runners/portability/stager.py b/sdks/python/apache_beam/runners/portability/stager.py
index 98c0e3176f75..abe60d37a63e 100644
--- a/sdks/python/apache_beam/runners/portability/stager.py
+++ b/sdks/python/apache_beam/runners/portability/stager.py
@@ -280,10 +280,11 @@ def create_job_resources(options,  # type: PipelineOptions
           raise RuntimeError(
               'The file %s cannot be found. It was specified in the '
               '--setup_file command line option.' % setup_options.setup_file)
-        if os.path.basename(setup_options.setup_file) != 'setup.py':
+        if (os.path.basename(setup_options.setup_file) != 'setup.py' and
+            os.path.basename(setup_options.setup_file) != 'pyproject.toml'):
           raise RuntimeError(
               'The --setup_file option expects the full path to a file named '
-              'setup.py instead of %s' % setup_options.setup_file)
+              'setup.py or pyproject.toml, got: %s' % setup_options.setup_file)
         tarball_file = Stager._build_setup_package(
             setup_options.setup_file, temp_dir, build_setup_args)
         resources.append(
diff --git a/sdks/python/test-suites/portable/common.gradle b/sdks/python/test-suites/portable/common.gradle
index 4f232c5b104f..f578319e5162 100644
--- a/sdks/python/test-suites/portable/common.gradle
+++ b/sdks/python/test-suites/portable/common.gradle
@@ -92,10 +92,11 @@ tasks.register("portableLocalRunnerJuliaSetWithSetupPy") {
           && cd ${pythonRootDir} \\
           && pip install -e . \\
           && cd apache_beam/examples/complete/juliaset \\
+          && pip install -e . \\
           && python juliaset_main.py \\
               --runner=PortableRunner \\
               --job_endpoint=embed \\
-              --setup_file=./setup.py \\
+              --setup_file=./pyproject.toml \\
               --coordinate_output=/tmp/juliaset \\
               --grid_size=1
           """
diff --git a/setup.py b/setup.py
new file mode 100644
index 000000000000..357f45596736
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,8 @@
+"""An optional setuptools configuration stub for the pipeline package.
+
+Use pyproject.toml to define the package. Add this file if you must
+use the --setup_file pipeline option on Beam 2.59.0 or earlier.
+"""
+
+import setuptools
+setuptools.setup()
diff --git a/website/www/site/content/en/documentation/sdks/python-pipeline-dependencies.md b/website/www/site/content/en/documentation/sdks/python-pipeline-dependencies.md
index 2a2a515ec09b..e13551658b3f 100644
--- a/website/www/site/content/en/documentation/sdks/python-pipeline-dependencies.md
+++ b/website/www/site/content/en/documentation/sdks/python-pipeline-dependencies.md
@@ -108,7 +108,7 @@ Often, your pipeline code spans multiple files. To run your project remotely, yo
           # List Python packages your pipeline depends on.
         ]
 
-2. If your package requires if some programmatic configuration, or you need to use the `--setup_file` pipeline option, create a setup.py file for your project.
+2. If your package requires if some programmatic configuration, or you need to use the `--setup_file` pipeline option on Beam SDK 2.59.0 or earlier, create a setup.py file for your project.
 
         # Note that the package can be completely defined by pyproject.toml.
         # This file is optional.
@@ -137,7 +137,8 @@ Often, your pipeline code spans multiple files. To run your project remotely, yo
 
 6. Run your pipeline with the following command-line option:
 
-        --setup_file /path/to/setup.py
+        --setup_file /path/to/setup.py OR
+        --setup_file /path/to/pyproject.toml (requires Beam SDK 2.60.0 or later).
 
 **Note:** It is not necessary to supply the `--requirements_file` [option](#pypi-dependencies) if the dependencies of your package are defined in the
 `dependencies` field of the `pyproject.toml` file (see step 1). However unlike with the `--requirements_file` option, when you use the `--setup_file` option, Beam doesn't stage the dependent packages to the runner.
@@ -147,19 +148,6 @@ Only the pipeline package is staged. If they aren't already provided in the runt
 ## Non-Python Dependencies or PyPI Dependencies with Non-Python Dependencies {#nonpython}
 
 If your pipeline uses non-Python packages, such as packages that require installation using the `apt install` command, or uses a PyPI package that depends on non-Python dependencies during package installation, we recommend installing them using a [custom container](#custom-containers).
-Otherwise, you must perform the following steps.
-
-1. [Structure your pipeline as a package](#multiple-file-dependencies).
-
-2. Add the required installation commands for the non-Python dependencies, such as the `apt install` commands, to the list of `CUSTOM_COMMANDS` in your `setup.py` file. See the [Juliaset setup.py file](https://github.com/apache/beam/blob/master/sdks/python/apache_beam/examples/complete/juliaset/setup.py) for an example.
-
-    **Note:** You must verify that these commands run on the remote worker. For example, if you use `apt`, the remote worker needs `apt` support.
-
-3. Run your pipeline with the following command-line option:
-
-        --setup_file /path/to/setup.py
-
-**Note:** Because custom commands execute after the dependencies for your workflow are installed (by `pip`), you should omit the PyPI package dependency from the pipeline's `requirements.txt` file and from the `install_requires` parameter in the `setuptools.setup()` call of your `setup.py` file.
 
 ## Pre-building SDK Container Image