diff --git a/tests/integration/endpoints/test_jobs.py b/tests/integration/endpoints/test_jobs.py
index b37cd67..546982c 100644
--- a/tests/integration/endpoints/test_jobs.py
+++ b/tests/integration/endpoints/test_jobs.py
@@ -13,6 +13,7 @@
 from workerfacing_api.core.filesystem import FileSystem, LocalFilesystem, S3Filesystem
 from workerfacing_api.core.queue import RDSJobQueue
 from workerfacing_api.crud import job_tracking
+from workerfacing_api.exceptions import JobDeletedException
 from workerfacing_api.schemas.queue_jobs import (
     AppSpecs,
     EnvironmentTypes,
@@ -277,7 +278,7 @@ def test_put_job_status_canceled(
         client.get(self.endpoint, params={"memory": 1})
 
         def mock_update_job(*args: Any, **kwargs: Any) -> None:
-            raise ValueError("Job not found")
+            raise JobDeletedException("Job not found")
 
         monkeypatch.setattr(job_tracking, "update_job", mock_update_job)
         res = client.put(f"{self.endpoint}/1/status", params={"status": "running"})
diff --git a/tests/unit/crud/__init__.py b/tests/unit/crud/__init__.py
new file mode 100644
index 0000000..deae50a
--- /dev/null
+++ b/tests/unit/crud/__init__.py
@@ -0,0 +1 @@
+# Empty init file
diff --git a/tests/unit/crud/test_job_tracking.py b/tests/unit/crud/test_job_tracking.py
new file mode 100644
index 0000000..9625282
--- /dev/null
+++ b/tests/unit/crud/test_job_tracking.py
@@ -0,0 +1,27 @@
+"""Tests for job_tracking module."""
+
+from unittest.mock import MagicMock, patch
+
+import pytest
+
+from workerfacing_api.crud.job_tracking import update_job
+from workerfacing_api.exceptions import JobDeletedException
+from workerfacing_api.schemas.rds_models import JobStates
+
+
+@patch("workerfacing_api.crud.job_tracking.requests.put")
+def test_update_job_raises_job_deleted_exception(mock_put: MagicMock) -> None:
+    """Test that update_job raises JobDeletedException on 404 response."""
+    # Mock a 404 response
+    mock_response = MagicMock()
+    mock_response.status_code = 404
+    mock_put.return_value = mock_response
+
+    job_id = 789
+
+    with pytest.raises(JobDeletedException) as exc_info:
+        update_job(job_id, JobStates.running)
+
+    assert f"Job {job_id} not found; it was probably deleted by the user." in str(
+        exc_info.value
+    )
diff --git a/workerfacing_api/core/queue.py b/workerfacing_api/core/queue.py
index dcbd91b..a9e668b 100644
--- a/workerfacing_api/core/queue.py
+++ b/workerfacing_api/core/queue.py
@@ -18,6 +18,7 @@
 
 from workerfacing_api import settings
 from workerfacing_api.crud import job_tracking
+from workerfacing_api.exceptions import JobDeletedException, JobNotAssignedException
 from workerfacing_api.schemas.queue_jobs import (
     EnvironmentTypes,
     JobFilter,
@@ -457,7 +458,7 @@ def pop(self, environment: EnvironmentTypes, receipt_handle: str) -> bool:
                 job.workers = ";".join(job.workers.split(";") + [hostname])
                 try:
                     self._update_job_status(session, job, status=JobStates.pulled)
-                except ValueError:
+                except JobDeletedException:
                     # job probably deleted by user
                     return False
             return True
@@ -484,7 +485,7 @@ def get_job(
         if hostname:
             workers = job.workers.split(";")
             if not workers or hostname != workers[-1]:
-                raise ValueError(
+                raise JobNotAssignedException(
                     f"Job with id {job_id} is not assigned to worker {hostname}"
                 )
         return job
@@ -505,11 +506,11 @@ def _update_job_status(
             job_id = job.job["meta"]["job_id"]
             assert isinstance(job_id, int)
             job_tracking.update_job(job_id, status, runtime_details)
-        except ValueError as e:
+        except JobDeletedException as e:
             # job probably deleted by user
             session.delete(job)
             session.commit()
-            raise ValueError(f"Could not update job, probably deleted by user: {e}")
+            raise e from e
 
     def update_job_status(
         self,
@@ -545,19 +546,27 @@ def handle_timeouts(
                 # TODO: increase priority?
                 job.num_retries += 1
                 session.add(job)
-                self.update_job_status(
-                    job.id,
-                    JobStates.queued,
-                    f"timeout {job.num_retries} (workers tried: {job.workers})",
-                )
-                n_retry += 1
+                try:
+                    self.update_job_status(
+                        job.id,
+                        JobStates.queued,
+                        f"timeout {job.num_retries} (workers tried: {job.workers})",
+                    )
+                    n_retry += 1
+                except JobDeletedException:
+                    # job probably deleted by user, skip updating status
+                    pass
             jobs_failed = jobs_timeout.filter(QueuedJob.num_retries >= max_retries)
             for job in jobs_failed:
-                self.update_job_status(
-                    job.id,
-                    JobStates.error,
-                    "max retries reached",
-                )
-                n_failed += 1
+                try:
+                    self.update_job_status(
+                        job.id,
+                        JobStates.error,
+                        "max retries reached",
+                    )
+                    n_failed += 1
+                except JobDeletedException:
+                    # job probably deleted by user, skip updating status
+                    pass
             session.commit()
         return n_retry, n_failed
diff --git a/workerfacing_api/crud/job_tracking.py b/workerfacing_api/crud/job_tracking.py
index a332ddc..233d835 100644
--- a/workerfacing_api/crud/job_tracking.py
+++ b/workerfacing_api/crud/job_tracking.py
@@ -2,6 +2,7 @@
 from fastapi.encoders import jsonable_encoder
 
 import workerfacing_api.settings as settings
+from workerfacing_api.exceptions import JobDeletedException
 from workerfacing_api.schemas.rds_models import JobStates
 
 
@@ -19,7 +20,7 @@ def update_job(
         headers={"x-api-key": settings.internal_api_key_secret},
     )
     if resp.status_code == 404:
-        raise ValueError(
+        raise JobDeletedException(
             f"Job {job_id} not found; it was probably deleted by the user."
         )
     resp.raise_for_status()
diff --git a/workerfacing_api/endpoints/jobs.py b/workerfacing_api/endpoints/jobs.py
index 6c52ba4..06eea1f 100644
--- a/workerfacing_api/endpoints/jobs.py
+++ b/workerfacing_api/endpoints/jobs.py
@@ -17,6 +17,7 @@
 from workerfacing_api.core.filesystem import FileSystem
 from workerfacing_api.core.queue import RDSJobQueue
 from workerfacing_api.dependencies import filesystem_dep, queue_dep
+from workerfacing_api.exceptions import JobDeletedException, JobNotAssignedException
 from workerfacing_api.schemas.files import FileHTTPRequest
 from workerfacing_api.schemas.queue_jobs import (
     EnvironmentTypes,
@@ -111,7 +112,7 @@ async def put_job_status(
     hostname = request.state.current_user.username
     try:
         queue.update_job_status(job_id, status, runtime_details, hostname=hostname)
-    except ValueError:
+    except (JobDeletedException, JobNotAssignedException):
         # acts as a "cancel job" signal to worker
         raise HTTPException(status_code=httpstatus.HTTP_404_NOT_FOUND)
 
diff --git a/workerfacing_api/exceptions.py b/workerfacing_api/exceptions.py
new file mode 100644
index 0000000..354cde8
--- /dev/null
+++ b/workerfacing_api/exceptions.py
@@ -0,0 +1,13 @@
+"""Custom exceptions for the workerfacing API."""
+
+
+class JobDeletedException(Exception):
+    """Exception raised when a job has been deleted by the user."""
+
+    pass
+
+
+class JobNotAssignedException(Exception):
+    """Exception raised when a job is not assigned to the current user."""
+
+    pass