diff --git a/tests/tools/test_base_environment.py b/tests/tools/test_base_environment.py
index 913ad0387c54..0368fb6cdaa2 100644
--- a/tests/tools/test_base_environment.py
+++ b/tests/tools/test_base_environment.py
@@ -130,6 +130,32 @@ def test_unique_delimiter_each_call(self):
 
 
 class TestInitSessionFailure:
+    def test_init_session_bootstrap_changes_to_configured_cwd(self):
+        env = _TestableEnv(cwd="/tmp/configured")
+
+        calls = []
+
+        def mock_run_bash(cmd, *, login=False, timeout=120, stdin_data=None):
+            calls.append({"cmd": cmd, "login": login})
+            return MagicMock()
+
+        env._run_bash = mock_run_bash
+        env._wait_for_process = MagicMock(
+            return_value={
+                "output": f"{env._cwd_marker}/tmp/configured{env._cwd_marker}",
+                "returncode": 0,
+            }
+        )
+        env.init_session()
+
+        assert len(calls) == 1
+        assert calls[0]["login"] is True
+        assert (
+            "cd /tmp/configured" in calls[0]["cmd"]
+            or "cd '/tmp/configured'" in calls[0]["cmd"]
+        )
+        assert env._snapshot_ready is True
+
     def test_snapshot_ready_false_on_failure(self):
         env = _TestableEnv()
 
@@ -147,16 +173,18 @@ def test_login_flag_when_snapshot_not_ready(self):
         env._snapshot_ready = False
 
         calls = []
+
         def mock_run_bash(cmd, *, login=False, timeout=120, stdin_data=None):
             calls.append({"login": login})
-            # Return a mock process handle
-            mock = MagicMock()
-            mock.poll.return_value = 0
-            mock.returncode = 0
-            mock.stdout = iter([])
-            return mock
+            return MagicMock()
 
         env._run_bash = mock_run_bash
+        env._wait_for_process = MagicMock(
+            return_value={
+                "output": f"{env._cwd_marker}/tmp{env._cwd_marker}",
+                "returncode": 0,
+            }
+        )
         env.execute("echo test")
 
         assert len(calls) == 1
diff --git a/tools/environments/base.py b/tools/environments/base.py
index d89b66f19de9..92ecc1e92eb9 100644
--- a/tools/environments/base.py
+++ b/tools/environments/base.py
@@ -299,6 +299,11 @@ def __init__(self, cwd: str, timeout: int, env: dict = None):
         self._cwd_marker = _cwd_marker(self._session_id)
         self._snapshot_ready = False
 
+    @staticmethod
+    def _quote_cwd_for_shell(cwd: str) -> str:
+        """Quote a cwd for shell ``cd`` while preserving ``~`` expansion."""
+        return shlex.quote(cwd) if cwd != "~" and not cwd.startswith("~/") else cwd
+
     # ------------------------------------------------------------------
     # Abstract methods
     # ------------------------------------------------------------------
@@ -335,6 +340,7 @@ def init_session(self):
         instead of running with ``bash -l``.
         """
         # Full capture: env vars, functions (filtered), aliases, shell options.
+        quoted_cwd = self._quote_cwd_for_shell(self.cwd)
         bootstrap = (
             f"export -p > {self._snapshot_path}\n"
             f"declare -f | grep -vE '^_[^_]' >> {self._snapshot_path}\n"
@@ -342,6 +348,7 @@ def init_session(self):
             f"echo 'shopt -s expand_aliases' >> {self._snapshot_path}\n"
             f"echo 'set +e' >> {self._snapshot_path}\n"
             f"echo 'set +u' >> {self._snapshot_path}\n"
+            f"cd {quoted_cwd} || exit 126\n"
             f"pwd -P > {self._cwd_file} 2>/dev/null || true\n"
             f"printf '\\n{self._cwd_marker}%s{self._cwd_marker}\\n' \"$(pwd -P)\"\n"
         )
@@ -380,9 +387,7 @@ def _wrap_command(self, command: str, cwd: str) -> str:
             parts.append(f"source {self._snapshot_path} 2>/dev/null || true")
 
         # cd to working directory — let bash expand ~ natively
-        quoted_cwd = (
-            shlex.quote(cwd) if cwd != "~" and not cwd.startswith("~/") else cwd
-        )
+        quoted_cwd = self._quote_cwd_for_shell(cwd)
         parts.append(f"builtin cd {quoted_cwd} || exit 126")
 
         # Run the actual command