diff --git a/autosubmit/job/job_list.py b/autosubmit/job/job_list.py
index 22245c23aa12b858e1537e613cb7f00aecfb7c01..bbc536e00aad7e421f4d306a9abd0108f77a9756 100644
--- a/autosubmit/job/job_list.py
+++ b/autosubmit/job/job_list.py
@@ -1190,7 +1190,9 @@ class JobList(object):
                     edge_added = True
             if parent.section == job.section:
                 self.actual_job_depends_on_special_chunk = True
-            if edge_added:
+
+            # Only fill this if, per example, jobs.A.Dependencies.A or jobs.A.Dependencies.A-N is set.
+            if edge_added and job.section in dependencies_keys_without_special_chars:
                 if job.name not in self.depends_on_previous_special_section:
                     self.depends_on_previous_special_section[job.name] = set()
                 if job.section not in self.depends_on_previous_special_section:
@@ -1207,6 +1209,25 @@ class JobList(object):
 
         return special_dependencies, problematic_dependencies
 
+    def get_filters_to_apply(self, job, dependency):
+        filters_to_apply = self._filter_current_job(job, copy.deepcopy(dependency.relationships))
+        filters_to_apply.pop("STATUS", None)
+        # Don't do perform special filter if only "FROM_STEP" is applied
+        if "FROM_STEP" in filters_to_apply:
+            if filters_to_apply.get("CHUNKS_TO","none") == "none" and filters_to_apply.get("MEMBERS_TO","none") == "none" and filters_to_apply.get("DATES_TO","none") == "none" and filters_to_apply.get("SPLITS_TO","none") == "none":
+                filters_to_apply = {}
+        filters_to_apply.pop("FROM_STEP", None)
+
+        # If the selected filter is "natural" for all filters_to, trigger the natural dependency calculation
+        all_natural = True
+        for f_value in filters_to_apply.values():
+            if f_value.lower() != "natural":
+                all_natural = False
+                break
+        if all_natural:
+            filters_to_apply = {}
+        return filters_to_apply
+
     def _manage_job_dependencies(self, dic_jobs, job, date_list, member_list, chunk_list, dependencies_keys,
                                  dependencies,
                                  graph):
@@ -1341,9 +1362,8 @@ class JobList(object):
                                                                                  dependency)
             if skip:
                 continue
-            filters_to_apply = self._filter_current_job(job, copy.deepcopy(dependency.relationships))
-            filters_to_apply.pop("STATUS", None)
-            filters_to_apply.pop("FROM_STEP", None)
+            filters_to_apply = self.get_filters_to_apply(job, dependency)
+
             if len(filters_to_apply) > 0:
                 dependencies_of_that_section = dic_jobs.as_conf.jobs_data[dependency.section].get("DEPENDENCIES", {})
                 ## Adds the dependencies to the job, and if not possible, adds the job to the problematic_dependencies
diff --git a/test/unit/test_dependencies.py b/test/unit/test_dependencies.py
index 2bb91211140c68715fdf0084864c773dcb2dacb9..054728dcb536082fd37458726a39b7311313917b 100644
--- a/test/unit/test_dependencies.py
+++ b/test/unit/test_dependencies.py
@@ -8,6 +8,7 @@ import unittest
 from copy import deepcopy
 from datetime import datetime
 from mock import patch
+from mock.mock import MagicMock
 
 from autosubmit.job.job_dict import DicJobs
 from autosubmit.job.job import Job
@@ -436,6 +437,84 @@ class TestJobList(unittest.TestCase):
         job_list.add_special_conditions(job, special_conditions, filters_to_apply, parent2)
         self.assertEqual(len(job.edge_info.get("RUNNING", "")), 2)
 
+    def test_add_special_conditions_chunks_to_once(self):
+        # Method from job_list
+        job = Job("child", 1, Status.WAITING, 1)
+        job.section = "child_one"
+        job.date = datetime.strptime("20200128", "%Y%m%d")
+        job.member = "fc0"
+        job.chunk = 1
+        job.split = 1
+        job.splits = 1
+        job.max_checkpoint_step = 0
+
+        job_two = Job("child", 1, Status.WAITING, 1)
+        job_two.section = "child_one"
+        job_two.date = datetime.strptime("20200128", "%Y%m%d")
+        job_two.member = "fc0"
+        job_two.chunk = 2
+        job_two.split = 1
+        job_two.splits = 1
+        job_two.max_checkpoint_step = 0
+
+        special_conditions = {"STATUS": "RUNNING", "FROM_STEP": "1"}
+        special_conditions_two = {"STATUS": "RUNNING", "FROM_STEP": "2"}
+
+        parent = Job("parent", 1, Status.RUNNING, 1)
+        parent.section = "parent_one"
+        parent.date = datetime.strptime("20200128", "%Y%m%d")
+        parent.member = None
+        parent.chunk = None
+        parent.split = None
+        parent.splits = None
+        parent.max_checkpoint_step = 0
+        job.status = Status.WAITING
+        job_two.status = Status.WAITING
+
+        job_list = Mock(wraps=self.JobList)
+        job_list._job_list = [job, job_two, parent]
+
+        dependency = MagicMock()
+        dependency.relationships = {'CHUNKS_FROM': {'1': {'FROM_STEP': '1'}, '2': {'FROM_STEP': '2'}, }, 'STATUS': 'RUNNING'}
+        filters_to_apply = job_list.get_filters_to_apply(job, dependency)
+        filters_to_apply_two = job_list.get_filters_to_apply(job_two, dependency)
+
+        assert filters_to_apply == {}
+        assert filters_to_apply_two == {}
+
+        job_list.add_special_conditions(job, special_conditions, filters_to_apply, parent)
+        job_list.add_special_conditions(job_two, special_conditions_two, filters_to_apply_two, parent)
+
+        dependency = MagicMock()
+        dependency.relationships = {'CHUNKS_FROM': {'1': {'FROM_STEP': '1', 'CHUNKS_TO':'natural'}, '2': {'FROM_STEP': '2', 'CHUNKS_TO':'natural'}, }, 'STATUS': 'RUNNING'}
+        filters_to_apply = job_list.get_filters_to_apply(job, dependency)
+        filters_to_apply_two = job_list.get_filters_to_apply(job_two, dependency)
+
+        assert filters_to_apply == {}
+        assert filters_to_apply_two == {}
+
+        job_list.add_special_conditions(job, special_conditions, filters_to_apply, parent)
+        job_list.add_special_conditions(job_two, special_conditions_two, filters_to_apply_two, parent)
+
+        self.assertEqual(job.max_checkpoint_step, 1)
+        self.assertEqual(job_two.max_checkpoint_step, 2)
+
+        value = job.edge_info.get("RUNNING", "").get("parent", ())
+        self.assertEqual((value[0].name, value[1]), (parent.name, "1"))
+        self.assertEqual(len(job.edge_info.get("RUNNING", "")), 1)
+
+        value_two = job_two.edge_info.get("RUNNING", "").get("parent", ())
+        self.assertEqual((value_two[0].name, value_two[1]), (parent.name, "2"))
+        self.assertEqual(len(job_two.edge_info.get("RUNNING", "")), 1)
+
+        dependency = MagicMock()
+        dependency.relationships = {'CHUNKS_FROM': {'1': {'FROM_STEP': '1', 'CHUNKS_TO':'natural', 'DATES_TO': "dummy"}, '2': {'FROM_STEP': '2', 'CHUNKS_TO':'natural', 'DATES_TO': "dummy"}, }, 'STATUS': 'RUNNING'}
+        filters_to_apply = job_list.get_filters_to_apply(job, dependency)
+        filters_to_apply_two = job_list.get_filters_to_apply(job_two, dependency)
+
+        assert filters_to_apply == {'CHUNKS_TO': 'natural', 'DATES_TO': 'dummy'}
+        assert filters_to_apply_two == {'CHUNKS_TO': 'natural', 'DATES_TO': 'dummy'}
+
     @patch('autosubmit.job.job_dict.date2str')
     def test_jobdict_get_jobs_filtered(self, mock_date2str):
         # Test the get_jobs_filtered function