diff --git a/src/python/pants/ng/subsystem_mypy_plugin.py b/src/python/pants/ng/subsystem_mypy_plugin.py
index dfd9ea6a32d..e36a01dfc33 100644
--- a/src/python/pants/ng/subsystem_mypy_plugin.py
+++ b/src/python/pants/ng/subsystem_mypy_plugin.py
@@ -11,10 +11,9 @@
     ClassDef,
     Decorator,
     FuncDef,
-    MypyFile,
     Statement,
 )
-from mypy.plugin import Plugin
+from mypy.plugin import ClassDefContext, Plugin
 
 
 def _has_option_decorator(node: Decorator) -> bool:
@@ -42,13 +41,28 @@ def _process_defns(defns: list[Statement]) -> None:
                 _process_defns(defn.func.body.body)
 
 
+def _process_subclass_hook(ctx: ClassDefContext) -> None:
+    _process_defns(ctx.cls.defs.body)
+
+
+# NB: If we create more intermediate subclasses, they must be added here.
+_SUBSYSTEM_BASE_CLASSES = frozenset(
+    {
+        "pants.ng.subsystem.SubsystemNg",
+        "pants.ng.subsystem.UniversalSubsystem",
+        "pants.ng.subsystem.ContextualSubsystem",
+        "pants.ng.goal.GoalSubsystemNg",
+    }
+)
+
+
 class SubsystemPlugin(Plugin):
-    """Mypy plugin that processes files to find methods decorated with @option."""
+    """Mypy plugin that processes SubsystemNg subclasses to find methods decorated with @option."""
 
-    def get_additional_deps(self, file: MypyFile) -> list[tuple[int, str, int]]:
-        """A file-level hook that we piggyback on to process the parsed file."""
-        _process_defns(file.defs)
-        return []
+    def get_base_class_hook(self, fullname: str):
+        if fullname in _SUBSYSTEM_BASE_CLASSES:
+            return _process_subclass_hook
+        return None
 
 
 def plugin(version: str) -> Type[Plugin]:
diff --git a/src/python/pants/ng/subsystem_mypy_plugin_test.py b/src/python/pants/ng/subsystem_mypy_plugin_test.py
new file mode 100644
index 00000000000..001e2ec236d
--- /dev/null
+++ b/src/python/pants/ng/subsystem_mypy_plugin_test.py
@@ -0,0 +1,91 @@
+# Copyright 2026 Pants project contributors (see CONTRIBUTORS.md).
+# Licensed under the Apache License, Version 2.0 (see LICENSE).
+
+import tempfile
+import textwrap
+from pathlib import Path
+
+import mypy.api
+
+from pants.util.contextutil import environment_as
+
+_FOO_GOAL_SUBSYSTEM_SOURCE = textwrap.dedent("""\
+    from pants.ng.goal import GoalSubsystemNg
+    from pants.ng.subsystem import option
+
+    class FooSubsystem(GoalSubsystemNg):
+        options_scope = "foo"
+        help = "Run foo"
+
+        @option(default=0, help="How much to foo")
+        def level(self) -> int: ...
+""")
+
+
+_BAR_SUBSYSTEM_SOURCE = textwrap.dedent("""\
+    from pants.ng.subsystem import ContextualSubsystem, option
+
+    class Bar(ContextualSubsystem):
+        options_scope = "bar"
+        help = "Options for bar."
+
+        @option(default="A", help="how to bar")
+        def how_to(self) -> str: ...
+
+        @option(default=false, help="whether to do the bar")
+        def do_it(self) -> bool: ...
+""")
+
+
+def _run_mypy(source: str, *, with_plugin: bool) -> tuple[str, str]:
+    """Run mypy on the given source string and return stdout."""
+    # SubsystemNg and its subclasses depend on various code from the
+    # codebase, so we must point mypy at it.
+    import pants
+
+    pants_src = str(Path(pants.__file__).parents[1])
+    plugin_path = str(Path(__file__).parent / "subsystem_mypy_plugin.py")
+
+    with (
+        tempfile.NamedTemporaryFile(suffix=".py", mode="w") as src_f,
+        tempfile.NamedTemporaryFile(suffix=".ini", mode="w") as cfg_f,
+    ):
+        src_f.write(source)
+        src_f.flush()
+        cfg_f.write("[mypy]\n")
+        cfg_f.flush()
+        with environment_as(MYPYPATH=pants_src):
+            args = [
+                src_f.name,
+                "--no-error-summary",
+                "--no-incremental",
+                f"--config-file={cfg_f.name}",
+            ]
+            if with_plugin:
+                args.extend(["--plugin", plugin_path])
+            stdout, stderr, _code = mypy.api.run(args)
+    return stdout, stderr
+
+
+def test_plugin_suppresses_empty_body_on_lint_subsystem() -> None:
+    stdout_noplugin, stderr_noplugin = _run_mypy(_FOO_GOAL_SUBSYSTEM_SOURCE, with_plugin=False)
+    assert "empty-body" in stdout_noplugin, (
+        f"Expected [empty-body] error without plugin:\n{stdout_noplugin} (err: {stderr_noplugin})"
+    )
+
+    stdout_plugin, stderr_plugin = _run_mypy(_FOO_GOAL_SUBSYSTEM_SOURCE, with_plugin=True)
+    assert "empty-body" not in stdout_plugin, (
+        f"Plugin did not suppress [empty-body] error:\n{stdout_plugin} (err: {stderr_plugin})"
+    )
+
+
+def test_plugin_suppresses_empty_body_on_contextual_subsystem() -> None:
+    stdout_noplugin, stderr_noplugin = _run_mypy(_BAR_SUBSYSTEM_SOURCE, with_plugin=False)
+    assert "empty-body" in stdout_noplugin, (
+        f"Expected [empty-body] error without plugin:\n{stdout_noplugin} (err: {stderr_noplugin})"
+    )
+
+    stdout_plugin, stderr_plugin = _run_mypy(_BAR_SUBSYSTEM_SOURCE, with_plugin=True)
+    assert "empty-body" not in stdout_plugin, (
+        f"Plugin did not suppress [empty-body] error:\n{stdout_plugin} (err: {stderr_plugin})"
+    )