diff --git a/doc/source/user/projectconf.rst b/doc/source/user/projectconf.rst
index f9017fbe..9f23cb16 100644
--- a/doc/source/user/projectconf.rst
+++ b/doc/source/user/projectconf.rst
@@ -103,6 +103,14 @@ configurations. Those can better be set with the :ref:`projectconf execconfig`.
     If a single worker is defined it will be used as default in the submission
     of new Flows.
 
+.. warning::
+
+    By default, jobflow-remote fetches the status of the jobs from the scheduler by
+    passing the list of ids. If the selected scheduler does not support this option
+    (e.g. SGE), it is also necessary to specify the username on the worker machine
+    through the ``scheduler_username`` option. Jobflow-remote will use that as a filter,
+    instead of the list of ids.
+
 .. _projectconf jobstore:
 
 JobStore
diff --git a/src/jobflow_remote/config/base.py b/src/jobflow_remote/config/base.py
index 2f6a136e..f228621d 100644
--- a/src/jobflow_remote/config/base.py
+++ b/src/jobflow_remote/config/base.py
@@ -177,6 +177,12 @@ class WorkerBase(BaseModel):
         None,
         description="Options for batch execution. If define the worker will be considered a batch worker",
     )
+    scheduler_username: Optional[str] = Field(
+        None,
+        description="If defined, the list of jobs running on the worker will be fetched based on the"
+        "username instead that from the list of job ids. May be necessary for some "
+        "scheduler_type (e.g. SGE)",
+    )
     model_config = ConfigDict(extra="forbid")
 
     @field_validator("scheduler_type")
diff --git a/src/jobflow_remote/jobs/runner.py b/src/jobflow_remote/jobs/runner.py
index 2855ba86..42cfe956 100644
--- a/src/jobflow_remote/jobs/runner.py
+++ b/src/jobflow_remote/jobs/runner.py
@@ -844,12 +844,18 @@ def check_run_status(self, filter: dict | None = None) -> None:  # noqa: A002
             if not ids_docs:
                 continue
 
+            worker = self.get_worker(worker_name)
+
             qjobs_dict = {}
             try:
                 ids_list = list(ids_docs)
                 queue = self.get_queue_manager(worker_name)
-                qjobs = queue.get_jobs_list(ids_list)
-                qjobs_dict = {qjob.job_id: qjob for qjob in qjobs}
+                qjobs = queue.get_jobs_list(
+                    jobs=ids_list, user=worker.scheduler_username
+                )
+                qjobs_dict = {
+                    qjob.job_id: qjob for qjob in qjobs if qjob.job_id in ids_list
+                }
             except Exception:
                 logger.warning(
                     f"error trying to get jobs list for worker: {worker_name}",
@@ -874,7 +880,6 @@ def check_run_status(self, filter: dict | None = None) -> None:  # noqa: A002
                         f"remote job with id {remote_doc['process_id']} is running"
                     )
                 elif qstate in [None, QState.DONE, QState.FAILED]:
-                    worker = self.get_worker(worker_name)
                     # if the worker is local go directly to DOWNLOADED, as files
                     # are not copied locally
                     if not worker.is_local:
@@ -995,8 +1000,12 @@ def update_batch_jobs(self) -> None:
             processes = list(batch_processes_data)
             queue_manager = self.get_queue_manager(worker_name)
             if processes:
-                qjobs = queue_manager.get_jobs_list(processes)
-                running_processes = {qjob.job_id for qjob in qjobs}
+                qjobs = queue_manager.get_jobs_list(
+                    jobs=processes, user=worker.scheduler_username
+                )
+                running_processes = {
+                    qjob.job_id for qjob in qjobs if qjob.job_id in processes
+                }
                 stopped_processes = set(processes) - running_processes
                 for pid in stopped_processes:
                     self.job_controller.remove_batch_process(pid, worker_name)
diff --git a/src/jobflow_remote/remote/queue.py b/src/jobflow_remote/remote/queue.py
index 9ce7645b..ec3e8ba3 100644
--- a/src/jobflow_remote/remote/queue.py
+++ b/src/jobflow_remote/remote/queue.py
@@ -220,6 +220,10 @@ def get_jobs_list(
         user: str | None = None,
         timeout: int | None = None,
     ) -> list[QJob]:
+        # in order to avoid issues with schedulers that do not support query by
+        # list of job ids, if the user is passed ignore the job ids.
+        if user is not None:
+            jobs = None
         job_cmd = self.scheduler_io.get_jobs_list_cmd(jobs, user)
         stdout, stderr, returncode = self.execute_cmd(job_cmd, timeout=timeout)
         return self.scheduler_io.parse_jobs_list_output(
diff --git a/tests/integration/test_slurm.py b/tests/integration/test_slurm.py
index f7e2ce34..2d242fa4 100644
--- a/tests/integration/test_slurm.py
+++ b/tests/integration/test_slurm.py
@@ -305,3 +305,60 @@ def test_undefined_additional_stores(worker, job_controller) -> None:
         job_controller.count_jobs(states=[JobState.COMPLETED, JobState.REMOTE_ERROR])
         == 2
     )
+
+
+def test_submit_flow_with_scheduler_username(monkeypatch, job_controller) -> None:
+    from jobflow import Flow
+
+    from jobflow_remote import submit_flow
+    from jobflow_remote.jobs.runner import Runner
+    from jobflow_remote.jobs.state import FlowState, JobState
+    from jobflow_remote.remote.queue import QueueManager
+    from jobflow_remote.testing import add
+
+    remote_worker_name = "test_remote_worker"
+
+    job = add(1, 1)
+    flow = Flow([job])
+    submit_flow(flow, worker=remote_worker_name)
+
+    # modify the runner so that uses a patched version of the worker
+    # where the scheduler_username is set
+    runner = Runner()
+    patched_worker = runner.get_worker(remote_worker_name).model_copy()
+    patched_worker.scheduler_username = "jobflow"
+
+    def patched_get_worker(self, worker_name):
+        if worker_name != remote_worker_name:
+            return runner.workers[worker_name]
+        return patched_worker
+
+    # Patch the get_jobs_list function to ensure that it is called with
+    # the correct parameters.
+    patch_called = False
+    user_arg = None
+    orig_get_jobs_list = QueueManager.get_jobs_list
+
+    def patched_get_jobs_list(self, jobs=None, user=None, timeout=None):
+        nonlocal patch_called
+        nonlocal user_arg
+        patch_called = True
+        user_arg = user
+        return orig_get_jobs_list(self=self, jobs=jobs, user=user, timeout=timeout)
+
+    with monkeypatch.context() as m:
+        m.setattr(Runner, "get_worker", patched_get_worker)
+        m.setattr(QueueManager, "get_jobs_list", patched_get_jobs_list)
+        runner.run_all_jobs(max_seconds=30)
+
+    assert patch_called, "The patched method was not called"
+    assert (
+        user_arg == "jobflow"
+    ), f"The argument for user passed to QueueManager.get_jobs_list is '{user_arg}' instead of 'jobflow'"
+
+    assert (
+        job_controller.count_jobs(states=JobState.COMPLETED) == 1
+    ), f"Jobs not marked as completed, full job info:\n{job_controller.get_jobs({})}"
+    assert (
+        job_controller.count_flows(states=FlowState.COMPLETED) == 1
+    ), f"Flows not marked as completed, full flow info:\n{job_controller.get_flows({})}"