diff --git a/autosubmit/autosubmit.py b/autosubmit/autosubmit.py
index 16c71d182b33d9bebfefe0b6399c121b26b3de60..4e7e8a1066220cb8608d2f87a8ebce8b04a1666b 100644
--- a/autosubmit/autosubmit.py
+++ b/autosubmit/autosubmit.py
@@ -86,7 +86,7 @@ from typing import List
 import autosubmit.history.utils as HUtils
 import autosubmit.helpers.autosubmit_helper as AutosubmitHelper
 import autosubmit.statistics.utils as StatisticsUtils
-from autosubmit.helpers.utils import proccess_id, terminate_child_process
+from autosubmit.helpers.utils import proccess_id, terminate_child_process, check_jobs_file_exists
 
 from contextlib import suppress
 
@@ -1485,6 +1485,7 @@ class Autosubmit:
             signal.signal(signal.SIGINT, signal_handler)
             as_conf = AutosubmitConfig(expid, BasicConfig, YAMLParserFactory())
             as_conf.check_conf_files(True)
+
             project_type = as_conf.get_project_type()
             safetysleeptime = as_conf.get_safetysleeptime()
             Log.debug("The Experiment name is: {0}", expid)
@@ -2501,6 +2502,12 @@ class Autosubmit:
         save_2 = False
         wrapper_errors = {}
         any_job_submitted = False
+        # Check section jobs
+        if not only_wrappers and not inspect :
+            jobs_section = set([job.section for job in job_list.get_ready()])
+            for section in jobs_section:
+                if check_jobs_file_exists(as_conf, section):
+                    raise AutosubmitCritical(f"Job {self.name} does not have a correct template// template not found", 7014)
         try:
             for platform in platforms_to_test:
                 packager = JobPackager(as_conf, platform, job_list, hold=hold)
diff --git a/autosubmit/helpers/utils.py b/autosubmit/helpers/utils.py
index b712d1f2cfd61ee6830041f2f7fa93767126e68b..7ccca9cf89a6e60664192a305baa158ce13aa0f5 100644
--- a/autosubmit/helpers/utils.py
+++ b/autosubmit/helpers/utils.py
@@ -1,4 +1,3 @@
-import collections
 import subprocess
 import os
 import pwd
@@ -11,6 +10,30 @@ from autosubmit.notifications.notifier import Notifier
 from autosubmitconfigparser.config.basicconfig import BasicConfig
 from log.log import AutosubmitCritical, Log
 
+
+def check_jobs_file_exists(as_conf, current_section_name=None):
+    if str(as_conf.experiment_data.get("PROJECT", {}).get("PROJECT_TYPE", "none")).lower() != "none":
+        templates_dir = f"{as_conf.experiment_data.get('ROOTDIR','')}/proj/{as_conf.experiment_data.get('PROJECT', {}).get('PROJECT_DESTINATION', '')}"
+        if not os.path.exists(templates_dir):
+            raise AutosubmitCritical(f"Templates directory {templates_dir} does not exist", 7011)
+
+        # List of files that doesn't exist.
+        missing_files = ""
+        # Check if all files in jobs_data exist or only current section
+        if current_section_name:
+            jobs_data = [as_conf.jobs_data.get(current_section_name, {})]
+        else:
+            jobs_data = as_conf.jobs_data.values()
+        for data in jobs_data:
+            if "SCRIPT" not in data:
+                if "FILE" in data:
+                    if not os.path.exists(f"{templates_dir}/{data['FILE']}"):
+                        missing_files += f"{templates_dir}/{data['FILE']} \n"
+                    else:
+                        Log.result(f"File {templates_dir}/{data['FILE']} exists")
+        if missing_files:
+            raise AutosubmitCritical(f"Templates not found:\n{missing_files}", 7011)
+
 def terminate_child_process(expid, platform=None):
     # get pid of the main process
     pid = os.getpid()
diff --git a/autosubmit/job/job.py b/autosubmit/job/job.py
index 9b892d2671da93bcc4b9620a2b8c0cd0b6069029..bad576df257f0f7696f6546510c84029b7fc6b76 100644
--- a/autosubmit/job/job.py
+++ b/autosubmit/job/job.py
@@ -1995,8 +1995,9 @@ class Job(object):
         :rtype: str
         """
         self.update_parameters(as_conf, self.parameters)
-        if self.script and self.file:
-            Log.warning(f"Custom script for job {self.name} is being used, file contents are ignored.")
+        if self.script:
+            if self.file:
+                Log.warning(f"Custom script for job {self.name} is being used, file contents are ignored.")
             template = self.script
         else:
             try: