diff --git a/CHANGELOG.md b/CHANGELOG.md
index d71b6e65b2..15118f53e9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -58,6 +58,15 @@ END_UNRELEASED_TEMPLATE
 
 {#v0-0-0-changed}
 ### Changed
+* **DEPRECATED: implicit zipapp support**
+  * Implicit zipapp output of `py_binary`/`py_test` has been deprecated and
+    replaced by separate {obj}`py_zipapp_binary` and {obj}`py_zipapp_test`
+    rules. See
+    [#3567](https://github.com/bazel-contrib/rules_python/issues/3567)
+    for a detailed migration guide.
+* (toolchains) stop exposing config settings in python toolchain alias repos.
+  Please consider depending on the flags defined in
+  `//python/config_setting/...` and the `@platforms` package instead.
 * (binaries/tests) The `PYTHONBREAKPOINT` environment variable is automatically inherited
 * (binaries/tests) The {obj}`stamp` attribute now transitions the Bazel builtin
   {obj}`--stamp` flag.
diff --git a/python/features.bzl b/python/features.bzl
index 291de33d1a..4cc9436677 100644
--- a/python/features.bzl
+++ b/python/features.bzl
@@ -63,6 +63,14 @@ def _features_typedef():
     optional trailing `-rcN`. For unreleased versions, it is an empty string.
     :::{versionadded} 0.38.0
     ::::
+
+    ::::{field} zipapp_rules
+    :type: bool
+
+    Whether the rules_python version has the `py_zipapp_*` rules
+
+    :::{versionadded} VERSION_NEXT_FEATURE
+    ::::
     """
 
 features = struct(
@@ -73,4 +81,5 @@ features = struct(
     py_info_venv_symlinks = True,
     uses_builtin_rules = False,
     version = _VERSION_PRIVATE if "$Format" not in _VERSION_PRIVATE else "",
+    zipapp_rules = True,
 )
diff --git a/python/private/py_executable.bzl b/python/private/py_executable.bzl
index 9f1113d9f6..45a18abb05 100644
--- a/python/private/py_executable.bzl
+++ b/python/private/py_executable.bzl
@@ -379,6 +379,21 @@ def _create_executable(
     # When --build_python_zip is enabled, then the zip file becomes
     # one of the default outputs.
     if build_zip_enabled:
+        # buildifier: disable=print
+        print(
+            """
+======================================================================
+WARNING: Target: {}
+  The `--build_python_zip` flag and implicit zipapp output of `py_binary`
+  and `py_test` is deprecated and will be removed in a future release.
+  Switch to `py_zipapp_binary` or `py_zipapp_test`. For migration
+  instructions and guide, see:
+
+  https://github.com/bazel-contrib/rules_python/issues/3567
+======================================================================
+               """.rstrip().format(ctx.label),
+        )
+
         extra_default_outputs.append(zip_file)
 
     # The logic here is a bit convoluted. Essentially, there are 3 types of
diff --git a/python/private/zipapp/py_zipapp_rule.bzl b/python/private/zipapp/py_zipapp_rule.bzl
index a0f0df943f..e97e1a4171 100644
--- a/python/private/zipapp/py_zipapp_rule.bzl
+++ b/python/private/zipapp/py_zipapp_rule.bzl
@@ -218,6 +218,9 @@ def _py_zipapp_executable_impl(ctx):
             runfiles = ctx.runfiles(files = default_outputs),
             executable = executable,
         ),
+        OutputGroupInfo(
+            python_zip_file = depset([zip_file]),
+        ),
     ]
 
 def _transition_zipapp_impl(settings, attr):
@@ -325,10 +328,25 @@ Whether the output should be an executable zip file.
 
 _TOOLCHAINS = [EXEC_TOOLS_TOOLCHAIN_TYPE] + ([LAUNCHER_MAKER_TOOLCHAIN_TYPE] if rp_config.bazel_9_or_later else [])
 
+_COMMON_RULE_DOC = """
+
+Output groups:
+
+* `python_zip_file`: (*deprecated*) The plain, non-self-executable zipapp zipfile.
+  *This output group is deprecated and retained for compatibility with
+  the previous implicit zipapp functionality. Set `executable=False`
+  and use the default output of the target instead.*
+
+:::{versionadded} VERSION_NEXT_FEATURE
+:::
+""".lstrip()
+
 py_zipapp_binary = rule(
     doc = """
 Packages a `py_binary` as a Python zipapp.
-""",
+
+{}
+""".format(_COMMON_RULE_DOC),
     implementation = _py_zipapp_executable_impl,
     attrs = _ATTRS,
     # NOTE: While this is marked executable, it is conditionally executable
@@ -343,7 +361,9 @@ py_zipapp_test = rule(
 Packages a `py_test` as a Python zipapp.
 
 This target is also a valid test target to run.
-""",
+
+{}
+""".format(_COMMON_RULE_DOC),
     implementation = _py_zipapp_executable_impl,
     attrs = _ATTRS,
     # NOTE: While this is marked as a test, it is conditionally executable
diff --git a/python/zipapp/py_zipapp_binary.bzl b/python/zipapp/py_zipapp_binary.bzl
index 4c40786200..ba7652c6d4 100644
--- a/python/zipapp/py_zipapp_binary.bzl
+++ b/python/zipapp/py_zipapp_binary.bzl
@@ -1,4 +1,10 @@
-"""`py_zipapp_binary` macro."""
+"""`py_zipapp_binary` macro.
+
+:::{seealso}
+
+{obj}`features.zipapp_rules` to detect if this rule is available.
+:::
+"""
 
 load("//python/private:util.bzl", "add_tag")
 load("//python/private/zipapp:py_zipapp_rule.bzl", _py_zipapp_binary_rule = "py_zipapp_binary")
@@ -6,6 +12,9 @@ load("//python/private/zipapp:py_zipapp_rule.bzl", _py_zipapp_binary_rule = "py_
 def py_zipapp_binary(**kwargs):
     """Builds a Python zipapp from a py_binary/py_test target.
 
+    :::{versionadded} VERSION_NEXT_FEATURE
+    :::
+
     Args:
         **kwargs: Args passed onto {rule}`py_zipapp_binary`.
     """
diff --git a/python/zipapp/py_zipapp_test.bzl b/python/zipapp/py_zipapp_test.bzl
index bc113ad4ed..fa197701a9 100644
--- a/python/zipapp/py_zipapp_test.bzl
+++ b/python/zipapp/py_zipapp_test.bzl
@@ -1,4 +1,10 @@
-"""`py_zipapp_test` macro."""
+"""`py_zipapp_test` macro.
+
+:::{seealso}
+
+{obj}`features.zipapp_rules` to detect if this rule is available.
+:::
+"""
 
 load("//python/private:util.bzl", "add_tag")
 load("//python/private/zipapp:py_zipapp_rule.bzl", _py_zipapp_test = "py_zipapp_test")
@@ -6,6 +12,9 @@ load("//python/private/zipapp:py_zipapp_rule.bzl", _py_zipapp_test = "py_zipapp_
 def py_zipapp_test(**kwargs):
     """Builds a Python zipapp from a py_binary/py_test target.
 
+    :::{versionadded} VERSION_NEXT_FEATURE
+    :::
+
     Args:
         **kwargs: Args passed onto {rule}`py_zipapp_test`.
     """