diff --git a/docs/notes/2.23.x.md b/docs/notes/2.23.x.md
index 3270da0a9f4..5a179d1e6dc 100644
--- a/docs/notes/2.23.x.md
+++ b/docs/notes/2.23.x.md
@@ -134,6 +134,8 @@ Support documenting macro constants using `MY_CONSTANT: Annotated[some_type, Doc
 
 Fixed bug where files larger than 512KB were being materialized to a process's sandbox without write permissions if the file was only globbed by `output_directories=(".",)`.
 
+Fixed bug where using `RuleRunner` in plugin tests caused `ValueError` that complains about not finding build root sentinel files. Note that you may have to adjust your tests to account for the new `BUILDROOT` file that `RuleRunner` now injects in the sandbox it creates for each test. For example, a test that uses a `**` glob might have to add `!BUILDROOT` to exclude the `BUILDROOT` file, or otherwise account for its presence when inspecting a sandbox or its digest.
+
 ### Other minor tweaks
 
 The "Provided by" information in the documentation now correctly reflects the proper backend to enable to activate a certain feature.
diff --git a/pants-plugins/pants_explorer/server/graphql/query/conftest.py b/pants-plugins/pants_explorer/server/graphql/query/conftest.py
index 1d23cc8bc24..61b073c2055 100644
--- a/pants-plugins/pants_explorer/server/graphql/query/conftest.py
+++ b/pants-plugins/pants_explorer/server/graphql/query/conftest.py
@@ -42,16 +42,20 @@ def all_help_info(rule_runner: RuleRunner) -> AllHelpInfo:
     def fake_consumed_scopes_mapper(scope: str) -> tuple[str, ...]:
         return ("somescope", f"used_by_{scope or 'GLOBAL_SCOPE'}")
 
-    return HelpInfoExtracter.get_all_help_info(
-        options=rule_runner.options_bootstrapper.full_options(
-            rule_runner.build_config, union_membership=UnionMembership({})
-        ),
-        union_membership=rule_runner.union_membership,
-        consumed_scopes_mapper=fake_consumed_scopes_mapper,
-        registered_target_types=RegisteredTargetTypes.create(rule_runner.build_config.target_types),
-        build_symbols=BuildFileSymbolsInfo.from_info(),
-        build_configuration=rule_runner.build_config,
-    )
+    with rule_runner.pushd():
+        all_help_info = HelpInfoExtracter.get_all_help_info(
+            options=rule_runner.options_bootstrapper.full_options(
+                rule_runner.build_config, union_membership=UnionMembership({})
+            ),
+            union_membership=rule_runner.union_membership,
+            consumed_scopes_mapper=fake_consumed_scopes_mapper,
+            registered_target_types=RegisteredTargetTypes.create(
+                rule_runner.build_config.target_types
+            ),
+            build_symbols=BuildFileSymbolsInfo.from_info(),
+            build_configuration=rule_runner.build_config,
+        )
+    return all_help_info
 
 
 @pytest.fixture
diff --git a/pants-plugins/pants_explorer/server/graphql/query/targets.py b/pants-plugins/pants_explorer/server/graphql/query/targets.py
index e60f94e2304..2a8687bfad2 100644
--- a/pants-plugins/pants_explorer/server/graphql/query/targets.py
+++ b/pants-plugins/pants_explorer/server/graphql/query/targets.py
@@ -18,7 +18,14 @@
 from pants.help.help_info_extracter import TargetTypeHelpInfo
 from pants.util.strutil import softwrap
 
-specs_parser = SpecsParser()
+_specs_parser: SpecsParser | None = None
+
+
+def _get_specs_parser() -> SpecsParser:
+    global _specs_parser
+    if _specs_parser is None:
+        _specs_parser = SpecsParser()
+    return _specs_parser
 
 
 @strawberry.type(description="Describes a target field type.")
@@ -165,7 +172,7 @@ def target_types(
     async def targets(self, info: Info, query: Optional[TargetsQuery] = None) -> List[Target]:
         req = GraphQLContext.request_state_from_info(info).product_request
         specs = (
-            specs_parser.parse_specs(
+            _get_specs_parser().parse_specs(
                 query.specs, description_of_origin="GraphQL targets `query.specs`"
             )
             if query is not None and query.specs
diff --git a/pants-plugins/pants_explorer/server/graphql/query/targets_test.py b/pants-plugins/pants_explorer/server/graphql/query/targets_test.py
index 9194b6d4004..4dfedceb896 100644
--- a/pants-plugins/pants_explorer/server/graphql/query/targets_test.py
+++ b/pants-plugins/pants_explorer/server/graphql/query/targets_test.py
@@ -39,9 +39,13 @@ async def test_targets_query(
             "src/test/Dockerfile": "",
         }
     )
-    actual_result = await schema.execute(
-        queries, variable_values=variables, context_value=context, operation_name="TestTargetsQuery"
-    )
+    with rule_runner.pushd():
+        actual_result = await schema.execute(
+            queries,
+            variable_values=variables,
+            context_value=context,
+            operation_name="TestTargetsQuery",
+        )
     assert actual_result.errors is None
     assert actual_result.data == expected_data
 
diff --git a/src/python/pants/backend/project_info/BUILD b/src/python/pants/backend/project_info/BUILD
index b14525f43fe..558b0c5df43 100644
--- a/src/python/pants/backend/project_info/BUILD
+++ b/src/python/pants/backend/project_info/BUILD
@@ -3,4 +3,10 @@
 
 python_sources()
 
-python_tests(name="tests", timeout=180)
+python_tests(
+    name="tests",
+    timeout=180,
+    overrides={
+        "list_targets_test.py": {"dependencies": ["//BUILD_ROOT:files"]},
+    },
+)
diff --git a/src/python/pants/backend/project_info/dependencies_test.py b/src/python/pants/backend/project_info/dependencies_test.py
index fd260ee9e1f..971e9249720 100644
--- a/src/python/pants/backend/project_info/dependencies_test.py
+++ b/src/python/pants/backend/project_info/dependencies_test.py
@@ -109,11 +109,12 @@ def assert_dependencies(
             assert json.loads(result.stdout) == expected
     else:
         assert not result.stdout
-        with open(output_file) as f:
-            if output_format == DependenciesOutputFormat.text:
-                assert f.read().splitlines() == expected
-            elif output_format == DependenciesOutputFormat.json:
-                assert json.load(f) == expected
+        with rule_runner.pushd():
+            with open(output_file) as f:
+                if output_format == DependenciesOutputFormat.text:
+                    assert f.read().splitlines() == expected
+                elif output_format == DependenciesOutputFormat.json:
+                    assert json.load(f) == expected
 
 
 def test_no_target(rule_runner: PythonRuleRunner) -> None:
diff --git a/src/python/pants/backend/project_info/dependents_test.py b/src/python/pants/backend/project_info/dependents_test.py
index 3cb4d781a22..51b4cad464c 100644
--- a/src/python/pants/backend/project_info/dependents_test.py
+++ b/src/python/pants/backend/project_info/dependents_test.py
@@ -65,11 +65,12 @@ def assert_dependents(
             assert json.loads(result.stdout) == expected
     else:
         assert not result.stdout
-        with open(output_file) as f:
-            if output_format == DependentsOutputFormat.text:
-                assert f.read().splitlines() == expected
-            elif output_format == DependentsOutputFormat.json:
-                assert json.load(f) == expected
+        with rule_runner.pushd():
+            with open(output_file) as f:
+                if output_format == DependentsOutputFormat.text:
+                    assert f.read().splitlines() == expected
+                elif output_format == DependentsOutputFormat.json:
+                    assert json.load(f) == expected
 
 
 def test_no_targets(rule_runner: RuleRunner) -> None:
diff --git a/src/python/pants/backend/tools/taplo/rules_integration_test.py b/src/python/pants/backend/tools/taplo/rules_integration_test.py
index ecb88dee5cc..28aa9187311 100644
--- a/src/python/pants/backend/tools/taplo/rules_integration_test.py
+++ b/src/python/pants/backend/tools/taplo/rules_integration_test.py
@@ -42,7 +42,7 @@ def run_taplo(
     rule_runner.set_options(
         ["--backend-packages=pants.backend.tools.taplo", *(extra_args or ())],
     )
-    snapshot = rule_runner.request(Snapshot, [PathGlobs(["**"])])
+    snapshot = rule_runner.request(Snapshot, [PathGlobs(["**", "!BUILDROOT"])])
     partition = rule_runner.request(
         Partitions[Any], [TaploFmtRequest.PartitionRequest(snapshot.files)]
     )[0]
diff --git a/src/python/pants/base/BUILD b/src/python/pants/base/BUILD
index 614049541d9..98d5695f9e3 100644
--- a/src/python/pants/base/BUILD
+++ b/src/python/pants/base/BUILD
@@ -6,7 +6,9 @@ python_sources()
 python_tests(
     name="tests",
     sources=["*_test.py", "!exception_sink_test.py", "!*_integration_test.py"],
-    dependencies=["//BUILD_ROOT:files"],
+    overrides={
+        "build_root_test.py": {"dependencies": ["//BUILD_ROOT:files"]},
+    },
 )
 
 python_tests(
diff --git a/src/python/pants/bsp/testutil.py b/src/python/pants/bsp/testutil.py
index 3f39acd0dc0..f974ddedf58 100644
--- a/src/python/pants/bsp/testutil.py
+++ b/src/python/pants/bsp/testutil.py
@@ -95,7 +95,7 @@ def setup_bsp_server(
     notification_names = notification_names or set()
     thread_locals = PyThreadLocals.get_for_current_thread()
 
-    with setup_pipes() as pipes:
+    with setup_pipes() as pipes, rule_runner.pushd():
         context = BSPContext()
         rule_runner.set_session_values({BSPContext: context})
         conn = BSPConnection(
diff --git a/src/python/pants/core/goals/BUILD b/src/python/pants/core/goals/BUILD
index 37ae8dbc2d3..469511161ee 100644
--- a/src/python/pants/core/goals/BUILD
+++ b/src/python/pants/core/goals/BUILD
@@ -3,7 +3,13 @@
 
 python_sources()
 
-python_tests(name="tests", sources=["*_test.py", "!*_integration_test.py"])
+python_tests(
+    name="tests",
+    sources=["*_test.py", "!*_integration_test.py"],
+    overrides={
+        "publish_test.py": {"timeout": 70},
+    },
+)
 
 python_tests(
     name="integration",
diff --git a/src/python/pants/core/goals/check_test.py b/src/python/pants/core/goals/check_test.py
index 1be684cd3c4..ebbfc5d28fc 100644
--- a/src/python/pants/core/goals/check_test.py
+++ b/src/python/pants/core/goals/check_test.py
@@ -31,7 +31,7 @@
 )
 from pants.engine.target import FieldSet, MultipleSourcesField, Target, Targets
 from pants.engine.unions import UnionMembership
-from pants.testutil.option_util import create_options_bootstrapper, create_subsystem
+from pants.testutil.option_util import create_subsystem
 from pants.testutil.rule_runner import MockGet, RuleRunner, mock_console, run_rule_with_mocks
 from pants.util.logging import LogLevel
 from pants.util.meta import classproperty
@@ -157,8 +157,8 @@ def run_typecheck_rule(
 ) -> Tuple[int, str]:
     union_membership = UnionMembership({CheckRequest: request_types})
     check_subsystem = create_subsystem(CheckSubsystem, only=only or [])
-    with mock_console(create_options_bootstrapper(["-lwarn"])) as (console, stdio_reader):
-        rule_runner = RuleRunner()
+    rule_runner = RuleRunner(bootstrap_args=["-lwarn"])
+    with mock_console(rule_runner.options_bootstrapper) as (console, stdio_reader):
         result: Check = run_rule_with_mocks(
             check,
             rule_args=[
diff --git a/src/python/pants/core/goals/export_test.py b/src/python/pants/core/goals/export_test.py
index 2a99b88eb32..4146e9406a4 100644
--- a/src/python/pants/core/goals/export_test.py
+++ b/src/python/pants/core/goals/export_test.py
@@ -36,7 +36,7 @@
 from pants.engine.rules import QueryRule
 from pants.engine.target import Target, Targets
 from pants.engine.unions import UnionMembership, UnionRule
-from pants.testutil.option_util import create_options_bootstrapper, create_subsystem
+from pants.testutil.option_util import create_subsystem
 from pants.testutil.rule_runner import (
     MockEffect,
     MockGet,
@@ -90,7 +90,7 @@ def run_export_rule(rule_runner: RuleRunner, targets: List[Target]) -> Tuple[int
     union_membership = UnionMembership({ExportRequest: [MockExportRequest]})
     with open(os.path.join(rule_runner.build_root, "somefile"), "wb") as fp:
         fp.write(b"SOMEFILE")
-    with mock_console(create_options_bootstrapper()) as (console, stdio_reader):
+    with mock_console(rule_runner.options_bootstrapper) as (console, stdio_reader):
         digest = rule_runner.request(Digest, [CreateDigest([FileContent("foo/bar", b"BAR")])])
         result: Export = run_rule_with_mocks(
             export,
@@ -223,7 +223,7 @@ def test_warnings_for_non_local_target_environments(
     union_membership = UnionMembership({ExportRequest: [MockExportRequest]})
     with open(os.path.join(rule_runner.build_root, "somefile"), "wb") as fp:
         fp.write(b"SOMEFILE")
-    with mock_console(create_options_bootstrapper()) as (console, stdio_reader):
+    with mock_console(rule_runner.options_bootstrapper) as (console, stdio_reader):
         digest = rule_runner.request(Digest, [CreateDigest([FileContent("foo/bar", b"BAR")])])
         run_rule_with_mocks(
             export,
diff --git a/src/python/pants/core/goals/publish_test.py b/src/python/pants/core/goals/publish_test.py
index a389d5418cd..60ba1500571 100644
--- a/src/python/pants/core/goals/publish_test.py
+++ b/src/python/pants/core/goals/publish_test.py
@@ -183,9 +183,10 @@ def test_structured_output(rule_runner: RuleRunner) -> None:
         },
     ]
 
-    with open("published.json") as fd:
-        data = json.load(fd)
-        assert data == expected
+    with rule_runner.pushd():
+        with open("published.json") as fd:
+            data = json.load(fd)
+            assert data == expected
 
 
 @pytest.mark.skip("Can not run interactive process from test..?")
diff --git a/src/python/pants/engine/BUILD b/src/python/pants/engine/BUILD
index fd4c546cfe8..3a8c1c36dd1 100644
--- a/src/python/pants/engine/BUILD
+++ b/src/python/pants/engine/BUILD
@@ -8,6 +8,9 @@ python_tests(
     dependencies=["src/python/pants/engine/internals:fs_test_data"],
     sources=["*_test.py", "!streaming_workunit_handler_integration_test.py"],
     timeout=90,
+    overrides={
+        "goal_test.py": {"dependencies": ["//BUILD_ROOT:files"]},
+    },
 )
 
 python_tests(
diff --git a/src/python/pants/engine/fs_test.py b/src/python/pants/engine/fs_test.py
index 928856f276c..b3a88bc639c 100644
--- a/src/python/pants/engine/fs_test.py
+++ b/src/python/pants/engine/fs_test.py
@@ -112,6 +112,8 @@ def setup_fs_test_tar(rule_runner: RuleRunner) -> None:
             └── 2
         c.ln -> a/b
         d.ln -> a
+
+    NB: The RuleRunner injects a BUILDROOT file in the build_root.
     """
     data = pkgutil.get_data("pants.engine.internals", "fs_test_data/fs_test.tar")
     assert data is not None
@@ -123,6 +125,7 @@ def setup_fs_test_tar(rule_runner: RuleRunner) -> None:
 
 
 FS_TAR_ALL_FILES = (
+    "BUILDROOT",  # injected by RuleRunner, not present in tar
     "4.txt",
     "a/3.txt",
     "a/4.txt.ln",
@@ -221,7 +224,10 @@ def test_path_globs_glob_pattern(rule_runner: RuleRunner) -> None:
     )
     assert_path_globs(rule_runner, ["*/0.txt"], expected_files=[], expected_dirs=[])
     assert_path_globs(
-        rule_runner, ["*"], expected_files=["4.txt"], expected_dirs=["a", "c.ln", "d.ln"]
+        rule_runner,
+        ["*"],
+        expected_files=["BUILDROOT", "4.txt"],
+        expected_dirs=["a", "c.ln", "d.ln"],
     )
     assert_path_globs(
         rule_runner,
@@ -302,7 +308,7 @@ def test_path_globs_ignore_pattern(rule_runner: RuleRunner) -> None:
     assert_path_globs(
         rule_runner,
         ["**", "!*.ln"],
-        expected_files=["4.txt", "a/3.txt", "a/b/1.txt", "a/b/2"],
+        expected_files=["BUILDROOT", "4.txt", "a/3.txt", "a/b/1.txt", "a/b/2"],
         expected_dirs=["a", "a/b"],
     )
 
@@ -318,7 +324,7 @@ def test_path_globs_ignore_sock(rule_runner: RuleRunner) -> None:
     assert_path_globs(
         rule_runner,
         ["**"],
-        expected_files=["non-sock.txt"],
+        expected_files=["BUILDROOT", "non-sock.txt"],
         expected_dirs=[],
     )
 
diff --git a/src/python/pants/engine/internals/BUILD b/src/python/pants/engine/internals/BUILD
index f367f42787a..43030afe3f2 100644
--- a/src/python/pants/engine/internals/BUILD
+++ b/src/python/pants/engine/internals/BUILD
@@ -10,6 +10,7 @@ python_tests(
     sources=["*_test.py", "!scheduler_integration_test.py"],
     timeout=90,
     overrides={
+        "engine_test.py": {"dependencies": ["//BUILD_ROOT:files"]},
         "platform_rules_test.py": {"tags": ["platform_specific_behavior"], "timeout": 120},
     },
 )
diff --git a/src/python/pants/engine/internals/graph_test.py b/src/python/pants/engine/internals/graph_test.py
index 32073ddfbbc..b7ef88a8224 100644
--- a/src/python/pants/engine/internals/graph_test.py
+++ b/src/python/pants/engine/internals/graph_test.py
@@ -1779,7 +1779,7 @@ class SingleSourceSubclass(SingleSourceField):
         HydratedSources,
         [HydrateSourcesRequest(valid_sources, for_sources_types=[SourcesSubclass])],
     )
-    assert hydrated_valid_sources.snapshot.files == ("f1.f95",)
+    assert hydrated_valid_sources.snapshot.files == ("BUILDROOT", "f1.f95")
     assert hydrated_valid_sources.sources_type == SourcesSubclass
 
     valid_single_sources = SingleSourceSubclass("f1.f95", addr)
diff --git a/src/python/pants/engine/internals/specs_rules_test.py b/src/python/pants/engine/internals/specs_rules_test.py
index e544c6acd9b..aaf31c4877d 100644
--- a/src/python/pants/engine/internals/specs_rules_test.py
+++ b/src/python/pants/engine/internals/specs_rules_test.py
@@ -793,14 +793,21 @@ def assert_paths(
     )
     assert_paths(["demo/*.foo", "-demo/unowned.foo"], set(), set())
 
-    assert_paths([":"], {"f.txt"}, set())
+    assert_paths([":"], {"BUILDROOT", "f.txt"}, set())
     for dir_suffix in ("", ":"):
         assert_paths([f"unowned{dir_suffix}"], {"unowned/f.txt"}, {"unowned"})
         assert_paths([f"demo{dir_suffix}"], {*all_expected_demo_files, "demo/BUILD"}, {"demo"})
 
     assert_paths(
         ["::"],
-        {*all_expected_demo_files, "demo/BUILD", "f.txt", "unowned/f.txt", "unowned/subdir/f.txt"},
+        {
+            *all_expected_demo_files,
+            "BUILDROOT",
+            "demo/BUILD",
+            "f.txt",
+            "unowned/f.txt",
+            "unowned/subdir/f.txt",
+        },
         {"demo", "unowned", "unowned/subdir"},
     )
     assert_paths(
diff --git a/src/python/pants/source/filespec_test.py b/src/python/pants/source/filespec_test.py
index d6beac327ad..48e4fa71a71 100644
--- a/src/python/pants/source/filespec_test.py
+++ b/src/python/pants/source/filespec_test.py
@@ -48,7 +48,7 @@ def assert_rule_match(
         ("*/[be]*/b*", ("foo/bar/baz", "foo/bar/bar")),
         ("foo*/bar", ("foofighters/bar", "foofighters.venv/bar")),
         # Double stars.
-        ("**", ("a/b/c", "b")),
+        ("**", ("BUILDROOT", "a/b/c", "b")),
         ("a/**/f", ("a/f", "a/b/c/d/e/f")),
         ("a/b/**", ("a/b/d", "a/b/c/d/e/f")),
         # Dots.
diff --git a/src/python/pants/testutil/BUILD b/src/python/pants/testutil/BUILD
index da63ee45b78..c73b3375686 100644
--- a/src/python/pants/testutil/BUILD
+++ b/src/python/pants/testutil/BUILD
@@ -24,7 +24,6 @@ python_sources(
         "pants_integration_test.py": {
             "dependencies": ["//BUILD_ROOT:files", "src/python/pants/__main__.py"]
         },
-        "rule_runner.py": {"dependencies": ["//BUILD_ROOT:files"]},
     },
 )
 
diff --git a/src/python/pants/testutil/rule_runner.py b/src/python/pants/testutil/rule_runner.py
index a405e89fe4f..f3b8be43c01 100644
--- a/src/python/pants/testutil/rule_runner.py
+++ b/src/python/pants/testutil/rule_runner.py
@@ -31,6 +31,7 @@
     overload,
 )
 
+from pants.base.build_environment import get_buildroot
 from pants.base.build_root import BuildRoot
 from pants.base.specs_parser import SpecsParser
 from pants.build_graph.build_configuration import BuildConfiguration
@@ -310,17 +311,23 @@ def rewrite_rule_for_inherent_environment(rule):
         self.build_config = build_config_builder.create()
 
         self.environment = CompleteEnvironmentVars({})
-        self.options_bootstrapper = self.create_options_bootstrapper(args=bootstrap_args, env=None)
         self.extra_session_values = extra_session_values or {}
         self.inherent_environment = inherent_environment
         self.max_workunit_verbosity = max_workunit_verbosity
-        options = self.options_bootstrapper.full_options(
-            self.build_config,
-            union_membership=UnionMembership.from_rules(
-                rule for rule in self.rules if isinstance(rule, UnionRule)
-            ),
-        )
-        global_options = self.options_bootstrapper.bootstrap_options.for_global_scope()
+
+        # Change cwd and add sentinel file (BUILDROOT) so NativeOptionParser can find build_root.
+        with self.pushd():
+            Path("BUILDROOT").touch()
+            self.options_bootstrapper = self.create_options_bootstrapper(
+                args=bootstrap_args, env=None
+            )
+            options = self.options_bootstrapper.full_options(
+                self.build_config,
+                union_membership=UnionMembership.from_rules(
+                    rule for rule in self.rules if isinstance(rule, UnionRule)
+                ),
+            )
+            global_options = self.options_bootstrapper.bootstrap_options.for_global_scope()
 
         dynamic_remote_options, _ = DynamicRemoteOptions.from_options(options, self.environment)
         local_store_options = LocalStoreOptions.from_options(global_options)
@@ -398,7 +405,8 @@ def request(self, output_type: type[_O], inputs: Iterable[Any]) -> _O:
             if self.inherent_environment
             else Params(*inputs)
         )
-        result = assert_single_element(self.scheduler.product_request(output_type, [params]))
+        with self.pushd():
+            result = assert_single_element(self.scheduler.product_request(output_type, [params]))
         return cast(_O, result)
 
     def run_goal_rule(
@@ -413,10 +421,11 @@ def run_goal_rule(
         merged_args = (*(global_args or []), goal.name, *(args or []))
         self.set_options(merged_args, env=env, env_inherit=env_inherit)
 
-        raw_specs = self.options_bootstrapper.full_options_for_scopes(
-            [GlobalOptions.get_scope_info(), goal.subsystem_cls.get_scope_info()],
-            self.union_membership,
-        ).specs
+        with self.pushd():
+            raw_specs = self.options_bootstrapper.full_options_for_scopes(
+                [GlobalOptions.get_scope_info(), goal.subsystem_cls.get_scope_info()],
+                self.union_membership,
+            ).specs
         specs = SpecsParser(root_dir=self.build_root).parse_specs(
             raw_specs, description_of_origin="RuleRunner.run_goal_rule()"
         )
@@ -424,19 +433,25 @@ def run_goal_rule(
         stdout, stderr = StringIO(), StringIO()
         console = Console(stdout=stdout, stderr=stderr, use_colors=False, session=self.scheduler)
 
-        exit_code = self.scheduler.run_goal_rule(
-            goal,
-            Params(
-                specs,
-                console,
-                Workspace(self.scheduler),
-                *([self.inherent_environment] if self.inherent_environment else []),
-            ),
-        )
+        with self.pushd():
+            exit_code = self.scheduler.run_goal_rule(
+                goal,
+                Params(
+                    specs,
+                    console,
+                    Workspace(self.scheduler),
+                    *([self.inherent_environment] if self.inherent_environment else []),
+                ),
+            )
 
         console.flush()
         return GoalRuleResult(exit_code, stdout.getvalue(), stderr.getvalue())
 
+    @contextmanager
+    def pushd(self):
+        with pushd(self.build_root):
+            yield
+
     def create_options_bootstrapper(
         self, args: Iterable[str], env: Mapping[str, str] | None
     ) -> OptionsBootstrapper:
@@ -465,7 +480,8 @@ def set_options(
             **{k: os.environ[k] for k in (env_inherit or set()) if k in os.environ},
             **(env or {}),
         }
-        self.options_bootstrapper = self.create_options_bootstrapper(args=args, env=env)
+        with self.pushd():
+            self.options_bootstrapper = self.create_options_bootstrapper(args=args, env=env)
         self.environment = CompleteEnvironmentVars(env)
         self._set_new_session(self.scheduler.scheduler)
 
@@ -605,7 +621,7 @@ def write_digest(
         )
 
     def run_interactive_process(self, request: InteractiveProcess) -> InteractiveProcessResult:
-        with pushd(self.build_root):
+        with self.pushd():
             return native_engine.session_run_interactive_process(
                 self.scheduler.py_session,
                 request,
@@ -778,14 +794,15 @@ def mock_console(
     *,
     stdin_content: bytes | str | None = None,
 ) -> Iterator[tuple[Console, StdioReader]]:
-    global_bootstrap_options = options_bootstrapper.bootstrap_options.for_global_scope()
-    colors = (
-        options_bootstrapper.full_options_for_scopes(
-            [GlobalOptions.get_scope_info()], UnionMembership({}), allow_unknown_options=True
+    with pushd(get_buildroot()):
+        global_bootstrap_options = options_bootstrapper.bootstrap_options.for_global_scope()
+        colors = (
+            options_bootstrapper.full_options_for_scopes(
+                [GlobalOptions.get_scope_info()], UnionMembership({}), allow_unknown_options=True
+            )
+            .for_global_scope()
+            .colors
         )
-        .for_global_scope()
-        .colors
-    )
 
     with initialize_stdio(global_bootstrap_options), stdin_context(
         stdin_content
diff --git a/src/python/pants/vcs/git_test.py b/src/python/pants/vcs/git_test.py
index bca04d07907..843e4e85930 100644
--- a/src/python/pants/vcs/git_test.py
+++ b/src/python/pants/vcs/git_test.py
@@ -464,6 +464,7 @@ async def worktree_id_string() -> str:
                 QueryRule(str, []),
             ]
         )
+        rule_runner.build_root = origin.as_posix()
 
         rule_runner.set_options([], env_inherit={"PATH"})
         worktree_id_1 = rule_runner.request(str, [])
diff --git a/tests/python/pants_test/init/BUILD b/tests/python/pants_test/init/BUILD
index 855f5cff7ca..213100394fb 100644
--- a/tests/python/pants_test/init/BUILD
+++ b/tests/python/pants_test/init/BUILD
@@ -11,7 +11,8 @@ python_tests(
                 # These tests load `pants.toml`, which references many of these plugins.
                 "src/python/pants/bin:plugins",
             ],
-        }
+        },
+        "test_logging.py": {"dependencies": ["//BUILD_ROOT:files"]},
     },
 )
 
diff --git a/tests/python/pants_test/init/test_util.py b/tests/python/pants_test/init/test_util.py
index 9016f0d9f42..934a6ae4d94 100644
--- a/tests/python/pants_test/init/test_util.py
+++ b/tests/python/pants_test/init/test_util.py
@@ -14,8 +14,8 @@
 
 
 @contextmanager
-def physical_workdir_base() -> Iterator[OptionValueContainer]:
-    with temporary_dir(cleanup=False) as physical_workdir_base:
+def physical_workdir_base(rule_runner: RuleRunner) -> Iterator[OptionValueContainer]:
+    with temporary_dir(cleanup=False) as physical_workdir_base, rule_runner.pushd():
         bootstrap_options = create_options_bootstrapper(
             [f"--pants-physical-workdir-base={physical_workdir_base}"]
         ).bootstrap_options.for_global_scope()
@@ -42,7 +42,7 @@ def physical_workdir(pants_workdir: str, bootstrap_options: OptionValueContainer
 
 def test_init_workdir() -> None:
     rule_runner = RuleRunner()
-    with physical_workdir_base() as bootstrap_options:
+    with physical_workdir_base(rule_runner) as bootstrap_options:
         # Assert pants_workdir exists
         assert_exists(rule_runner.pants_workdir)