diff --git a/docs/upgrade.md b/docs/upgrade.md
index 943d9f41a1..46c83ea0f5 100644
--- a/docs/upgrade.md
+++ b/docs/upgrade.md
@@ -45,6 +45,8 @@ specify self upgrade --tag vX.Y.Z[suffix]
 
 Bare `specify self upgrade` executes immediately, matching the no-prompt behavior of commands like `pip install -U` and `npm update`. The CLI classifies your runtime into one of: `uv tool`, `pipx`, `uvx (ephemeral)`, source checkout, or unsupported. Only `uv tool` and `pipx` are upgraded automatically; for `uv tool` installs, it runs `uv tool install specify-cli --force --from <git ref>` under the hood so pinned release tags work. The other paths print path-specific guidance and exit 0 without touching anything.
 
+Tool detection recognizes current and legacy default installation directories, as well as directories configured with `UV_TOOL_DIR`, `PIPX_HOME`, or `XDG_DATA_HOME`. Keep the same directory environment variables set when upgrading a relocated installation so the installer also targets that location.
+
 Pinned tags must start with `vMAJOR.MINOR.PATCH`. Optional suffixes are limited to dev, alpha/beta/rc, and/or build metadata forms such as `v1.0.0-rc1`, `v0.8.0.dev0`, `v0.8.0+build.42`, or the combination `v1.0.0-rc1+build.42`; branch names, hash refs, `latest`, and bare versions without `v` are rejected.
 
 Set `SPECIFY_UPGRADE_TIMEOUT_SECS` to cap how long the installer subprocess may run (default: no timeout — interrupt with `Ctrl+C` if needed). If that internal timeout fires, `specify self upgrade` exits 124 and reports that it timed out while waiting for the installer subprocess, including the configured timeout and manual retry command. A real installer exit code 124 is propagated with `Upgrade failed. Installer exit code: 124.`, so scripts should treat exit 124 as ambiguous and inspect the message when they need to distinguish the two cases.
diff --git a/src/specify_cli/_version.py b/src/specify_cli/_version.py
index c8fcad7c7e..3e1e533284 100644
--- a/src/specify_cli/_version.py
+++ b/src/specify_cli/_version.py
@@ -182,11 +182,22 @@ def _render_argv(argv: list[str]) -> str:
 
 _INSTALLER_PATH_PREFIXES: dict[str, list[str]] = {
     "uv-tool": [
+        "${UV_TOOL_DIR}/specify-cli/",
+        "${XDG_DATA_HOME}/uv/tools/specify-cli/",
         "~/.local/share/uv/tools/specify-cli/",
+        "${APPDATA}/uv/tools/specify-cli/",
+        "${APPDATA}/uv/data/tools/specify-cli/",
+        "~/Library/Application Support/uv/tools/specify-cli/",
         "%LOCALAPPDATA%\\uv\\tools\\specify-cli\\",
     ],
     "pipx": [
+        "${PIPX_HOME}/venvs/specify-cli/",
+        "${XDG_DATA_HOME}/pipx/venvs/specify-cli/",
+        "~/.local/share/pipx/venvs/specify-cli/",
+        "~/Library/Application Support/pipx/venvs/specify-cli/",
+        "${LOCALAPPDATA}/pipx/pipx/venvs/specify-cli/",
         "~/.local/pipx/venvs/specify-cli/",
+        "~/pipx/venvs/specify-cli/",
         "%LOCALAPPDATA%\\pipx\\venvs\\specify-cli\\",
     ],
     "uvx-ephemeral": [
@@ -343,18 +354,25 @@ def _validate_tag(tag: str) -> str:
 def _expand_prefix(prefix: str) -> Path | None:
     """Expand `~` or `%LOCALAPPDATA%`-style tokens in a path prefix."""
 
-    expanded = os.path.expanduser(prefix)
+    # An unset or empty directory override must not become a root-level prefix.
+    for token in _UNRESOLVED_ENV_VAR_RE.findall(prefix):
+        if not os.environ.get(token.strip("${}%")):
+            return None
+    expanded = prefix
     if "%LOCALAPPDATA%" in expanded:
         local_app_data = os.environ.get("LOCALAPPDATA")
         if not local_app_data:
             return None
         expanded = expanded.replace("%LOCALAPPDATA%", local_app_data)
-    expanded = os.path.expandvars(expanded)
+    expanded = os.path.expanduser(os.path.expandvars(expanded))
     if _UNRESOLVED_ENV_VAR_RE.search(expanded):
         return None
     try:
         expanded_path = Path(expanded)
-        return expanded_path.resolve() if expanded_path.is_absolute() else expanded_path
+        # uv and pipx resolve their relative tool directories against the working directory.
+        if expanded_path.is_absolute() or prefix.startswith(("${UV_TOOL_DIR}/", "${PIPX_HOME}/")):
+            return expanded_path.resolve()
+        return expanded_path
     except OSError:
         return None
 
diff --git a/tests/specify_cli/test_version_detection.py b/tests/specify_cli/test_version_detection.py
index c769665920..897027934e 100644
--- a/tests/specify_cli/test_version_detection.py
+++ b/tests/specify_cli/test_version_detection.py
@@ -24,6 +24,130 @@
 )
 
 
+class TestRelocatedToolDetection:
+    @pytest.mark.parametrize("value", ["./tools", "../tools"])
+    @pytest.mark.parametrize("environment,expected", [
+        ("specify-cli", _InstallMethod.UV_TOOL),
+        ("specify-cli2", _InstallMethod.UNSUPPORTED),
+    ])
+    def test_relative_uv_tool_dir(self, monkeypatch, tmp_path, value, environment, expected):
+        working_dir = tmp_path / "working"
+        working_dir.mkdir()
+        monkeypatch.chdir(working_dir)
+        monkeypatch.setenv("UV_TOOL_DIR", value)
+        entrypoint = (working_dir / value / environment / "bin" / "specify").resolve()
+        entrypoint.parent.mkdir(parents=True)
+        entrypoint.write_text("#!/usr/bin/env python\n")
+        with patch("specify_cli._version._editable_marker_seen", return_value=False), patch(
+            "specify_cli._version.subprocess.run"
+        ) as registry_lookup:
+            assert _detect_install_method(str(entrypoint)) == expected
+        registry_lookup.assert_not_called()
+
+    @pytest.mark.parametrize("suffix", ["uv/tools/specify-cli/", "pipx/venvs/specify-cli/"])
+    def test_relative_xdg_data_home_is_not_accepted(self, monkeypatch, tmp_path, suffix):
+        from specify_cli._version import _expand_prefix, _path_is_within_prefix
+
+        monkeypatch.chdir(tmp_path)
+        monkeypatch.setenv("XDG_DATA_HOME", "./data")
+        prefix = _expand_prefix("${XDG_DATA_HOME}/" + suffix)
+        assert not _path_is_within_prefix((tmp_path / "data" / suffix / "bin/specify"), prefix)
+
+    @pytest.mark.parametrize("environment,expected", [
+        ("specify-cli", _InstallMethod.PIPX),
+        ("specify-cli2", _InstallMethod.UNSUPPORTED),
+    ])
+    def test_pipx_home_with_tilde(self, monkeypatch, tmp_path, environment, expected):
+        home = tmp_path / "home"
+        monkeypatch.setenv("HOME", str(home))
+        monkeypatch.setenv("USERPROFILE", str(home))
+        monkeypatch.setenv("PIPX_HOME", "~/pipx-home")
+        entrypoint = home / "pipx-home" / "venvs" / environment / "bin" / "specify"
+        entrypoint.parent.mkdir(parents=True)
+        entrypoint.write_text("#!/usr/bin/env python\n")
+        with patch("specify_cli._version._editable_marker_seen", return_value=False), patch(
+            "specify_cli._version.subprocess.run"
+        ) as registry_lookup:
+            assert _detect_install_method(str(entrypoint)) == expected
+        registry_lookup.assert_not_called()
+
+    @pytest.mark.parametrize("value", ["./pipx-home", "../pipx-home"])
+    @pytest.mark.parametrize("environment,expected", [
+        ("specify-cli", _InstallMethod.PIPX),
+        ("specify-cli2", _InstallMethod.UNSUPPORTED),
+    ])
+    def test_relative_pipx_home(self, monkeypatch, tmp_path, value, environment, expected):
+        working_dir = tmp_path / "working"
+        working_dir.mkdir()
+        monkeypatch.chdir(working_dir)
+        monkeypatch.setenv("PIPX_HOME", value)
+        entrypoint = (working_dir / value / "venvs" / environment / "bin" / "specify").resolve()
+        entrypoint.parent.mkdir(parents=True)
+        entrypoint.write_text("#!/usr/bin/env python\n")
+        with patch("specify_cli._version._editable_marker_seen", return_value=False), patch(
+            "specify_cli._version.subprocess.run"
+        ) as registry_lookup:
+            assert _detect_install_method(str(entrypoint)) == expected
+        registry_lookup.assert_not_called()
+
+    @pytest.mark.parametrize("env_name,suffix,method", [
+        ("UV_TOOL_DIR", "specify-cli/bin/specify", _InstallMethod.UV_TOOL),
+        ("XDG_DATA_HOME", "uv/tools/specify-cli/bin/specify", _InstallMethod.UV_TOOL),
+        ("APPDATA", "uv/data/tools/specify-cli/bin/specify", _InstallMethod.UV_TOOL),
+        ("APPDATA", "uv/tools/specify-cli/bin/specify", _InstallMethod.UV_TOOL),
+        ("HOME", "Library/Application Support/uv/tools/specify-cli/bin/specify", _InstallMethod.UV_TOOL),
+        ("PIPX_HOME", "venvs/specify-cli/bin/specify", _InstallMethod.PIPX),
+        ("XDG_DATA_HOME", "pipx/venvs/specify-cli/bin/specify", _InstallMethod.PIPX),
+        ("LOCALAPPDATA", "pipx/pipx/venvs/specify-cli/bin/specify", _InstallMethod.PIPX),
+        ("HOME", ".local/share/pipx/venvs/specify-cli/bin/specify", _InstallMethod.PIPX),
+        ("HOME", "Library/Application Support/pipx/venvs/specify-cli/bin/specify", _InstallMethod.PIPX),
+        ("HOME", "pipx/venvs/specify-cli/bin/specify", _InstallMethod.PIPX),
+    ])
+    def test_tool_directory_matches(self, monkeypatch, tmp_path, env_name, suffix, method):
+        root = tmp_path / "tool data"
+        monkeypatch.setenv(env_name, str(root))
+        if env_name == "HOME":
+            monkeypatch.setenv("USERPROFILE", str(root))
+        entrypoint = root / suffix
+        entrypoint.parent.mkdir(parents=True)
+        entrypoint.write_text("#!/usr/bin/env python\n")
+        with patch("specify_cli._version._editable_marker_seen", return_value=False), patch(
+            "specify_cli._version.subprocess.run"
+        ) as registry_lookup:
+            actual, signals = _detect_install_method(str(entrypoint), include_signals=True)
+        assert actual == method
+        assert signals.matched_tier == 1
+        registry_lookup.assert_not_called()
+
+    @pytest.mark.parametrize("env_name,suffix", [
+        ("UV_TOOL_DIR", "specify-cli2/bin/specify"),
+        ("APPDATA", "uv/tools/specify-cli2/bin/specify"),
+        ("HOME", "Library/Application Support/uv/tools/specify-cli2/bin/specify"),
+        ("XDG_DATA_HOME", "uv/tools/specify-cli2/bin/specify"),
+        ("PIPX_HOME", "venvs/specify-cli2/bin/specify"),
+    ])
+    def test_sibling_environment_is_not_accepted(self, monkeypatch, tmp_path, env_name, suffix):
+        monkeypatch.setenv(env_name, str(tmp_path))
+        if env_name == "HOME":
+            monkeypatch.setenv("USERPROFILE", str(tmp_path))
+        entrypoint = tmp_path / suffix
+        entrypoint.parent.mkdir(parents=True)
+        entrypoint.write_text("#!/usr/bin/env python\n")
+        with patch("specify_cli._version._editable_marker_seen", return_value=False):
+            assert _detect_install_method(str(entrypoint)) == _InstallMethod.UNSUPPORTED
+
+    @pytest.mark.parametrize("value", [None, ""])
+    @pytest.mark.parametrize("variable", ["UV_TOOL_DIR", "PIPX_HOME", "XDG_DATA_HOME"])
+    def test_unconfigured_prefix_is_ignored(self, monkeypatch, variable, value):
+        from specify_cli._version import _expand_prefix
+
+        if value is None:
+            monkeypatch.delenv(variable, raising=False)
+        else:
+            monkeypatch.setenv(variable, value)
+        assert _expand_prefix("${" + variable + "}/specify-cli/") is None
+
+
 class TestDetectionUvTool:
     """Tier-1 path-prefix detection for uv-tool installs."""