diff --git a/src/specify_cli/workflows/_commands.py b/src/specify_cli/workflows/_commands.py
index 973e69fe0..334c7e254 100644
--- a/src/specify_cli/workflows/_commands.py
+++ b/src/specify_cli/workflows/_commands.py
@@ -352,6 +352,7 @@ def workflow_run(
     from .catalog import WorkflowRegistry
 
     registered_id: str | None = None
+    registry_root = project_root
     if not is_file_source:
         # Reject path-equivalent spellings ("align-wf/", "align-wf/.") that
         # would miss the registry lookup yet still load the installed file,
@@ -364,16 +365,18 @@ def workflow_run(
         registered_id = source
     else:
         # A direct YAML path may still point at an installed workflow's own
-        # file; map it back to its ID so disabled state is enforced there too.
-        workflows_root = (project_root / ".specify" / "workflows").resolve()
+        # file; map it back to its owning project and ID from the canonical
+        # path itself so the guard is independent of the caller's cwd.
         resolved = source_path.resolve()
-        if resolved.is_relative_to(workflows_root):
-            rel_parts = resolved.relative_to(workflows_root).parts
-            if rel_parts:
-                registered_id = rel_parts[0]
+        parts = resolved.parts
+        for i in range(len(parts) - 2):
+            if parts[i] == ".specify" and parts[i + 1] == "workflows":
+                registry_root = Path(*parts[:i]) if i else Path(resolved.anchor or ".")
+                registered_id = parts[i + 2]
+                break
 
     if registered_id is not None:
-        installed_meta = WorkflowRegistry(project_root).get(registered_id)
+        installed_meta = WorkflowRegistry(registry_root).get(registered_id)
         if isinstance(installed_meta, dict) and not installed_meta.get("enabled", True):
             err.print(
                 f"[red]Error:[/red] Workflow '{_escape_markup(registered_id)}' is disabled. "
diff --git a/src/specify_cli/workflows/catalog.py b/src/specify_cli/workflows/catalog.py
index 942a6cfd0..87fe1ca0b 100644
--- a/src/specify_cli/workflows/catalog.py
+++ b/src/specify_cli/workflows/catalog.py
@@ -13,6 +13,7 @@ from __future__ import annotations
 import hashlib
 import json
 import os
+import tempfile
 import time
 from dataclasses import dataclass
 from pathlib import Path
@@ -85,15 +86,21 @@ class WorkflowRegistry:
     def save(self) -> None:
         """Persist registry to disk atomically."""
         self.workflows_dir.mkdir(parents=True, exist_ok=True)
-        # Write-then-replace so a failed dump cannot truncate the registry.
-        tmp_path = self.registry_path.with_name(self.registry_path.name + ".tmp")
+        # Unique, exclusive temp then replace: a failed dump cannot truncate
+        # the registry, a pre-created symlink cannot redirect the write, and
+        # concurrent CLI processes cannot collide on the same temp path.
+        fd, tmp = tempfile.mkstemp(
+            dir=str(self.registry_path.parent),
+            prefix=f".{self.registry_path.name}.",
+            suffix=".tmp",
+        )
         try:
-            with open(tmp_path, "w", encoding="utf-8") as f:
+            with os.fdopen(fd, "w", encoding="utf-8") as f:
                 json.dump(self.data, f, indent=2)
-            os.replace(tmp_path, self.registry_path)
-        except OSError:
+            os.replace(tmp, self.registry_path)
+        except BaseException:
             try:
-                tmp_path.unlink()
+                os.unlink(tmp)
             except OSError:
                 pass
             raise
diff --git a/tests/test_workflows.py b/tests/test_workflows.py
index 77589fb61..810a94dc3 100644
--- a/tests/test_workflows.py
+++ b/tests/test_workflows.py
@@ -8211,6 +8211,16 @@ steps:
         assert result.exit_code != 0
         assert "disabled" in result.output
 
+        # Same guard must hold when invoked from outside the project.
+        outside = project_dir.parent / "outside-cwd"
+        outside.mkdir(exist_ok=True)
+        monkeypatch.chdir(outside)
+        result = runner.invoke(
+            app, ["workflow", "run", str(project_dir / installed_yaml)]
+        )
+        assert result.exit_code != 0
+        assert "disabled" in result.output
+
     def test_disable_shows_marker_in_list(self, project_dir, monkeypatch):
         from typer.testing import CliRunner
         from specify_cli import app