diff --git a/test/unit/fair_data_station/fair_data_station_writer_test.rb b/test/unit/fair_data_station/fair_data_station_writer_test.rb
index deca179d80..0084bee6b3 100644
--- a/test/unit/fair_data_station/fair_data_station_writer_test.rb
+++ b/test/unit/fair_data_station/fair_data_station_writer_test.rb
@@ -458,12 +458,12 @@ class FairDataStationWriterTest < ActiveSupport::TestCase
     assert_equal 'test study 1', study.title
 
     expected = HashWithIndifferentAccess.new({
-      'Experimental site name':'manchester test site',
-      'study date details': {
-        'End date of Study': '2024-08-08',
-        'Start date of Study': '2024-08-01'
-      }
-    })
+                                               'Experimental site name': 'manchester test site',
+                                               'study date details': {
+                                                 'End date of Study': '2024-08-08',
+                                                 'Start date of Study': '2024-08-01'
+                                               }
+                                             })
 
     assert_equal expected, study.extended_metadata.data
 
@@ -472,7 +472,7 @@ class FairDataStationWriterTest < ActiveSupport::TestCase
     assert_equal 'test study 2', study.title
 
     expected = HashWithIndifferentAccess.new({
-                                               'Experimental site name':'manchester test site',
+                                               'Experimental site name': 'manchester test site',
                                                'study date details': {
                                                  'End date of Study': '2024-08-18',
                                                  'Start date of Study': '2024-08-10'
@@ -487,7 +487,7 @@ class FairDataStationWriterTest < ActiveSupport::TestCase
     assert_equal 'test obs unit 2', obs_unit.title
 
     expected = HashWithIndifferentAccess.new({
-                                               'Gender':'female',
+                                               'Gender': 'female',
                                                'obs_unit_birth_details': {
                                                  'Birth weight': '1235g',
                                                  'Date of birth': '2020-01-11'
@@ -522,7 +522,7 @@ class FairDataStationWriterTest < ActiveSupport::TestCase
     assert_equal 'test study 1', study.title
 
     expected = HashWithIndifferentAccess.new({
-                                               'Experimental site name':'manchester test site',
+                                               'Experimental site name': 'manchester test site',
                                                'child': {
                                                  'End date of Study': '2024-08-08',
                                                  'grandchild': {
@@ -534,6 +534,103 @@ class FairDataStationWriterTest < ActiveSupport::TestCase
     assert_equal expected, study.extended_metadata.data
   end
 
+  test 'update isa with nested metadata' do
+    FactoryBot.create(:fairdata_test_case_investigation_extended_metadata)
+    study_emt = FactoryBot.create(:fairdata_test_case_nested_study_extended_metadata)
+    obs_unit_emt = FactoryBot.create(:fairdata_test_case_nested_obsv_unit_extended_metadata)
+    FactoryBot.create(:fairdata_test_case_assay_extended_metadata)
+    FactoryBot.create(:fairdatastation_test_case_sample_type)
+    FactoryBot.create(:experimental_assay_class)
+    path = "#{Rails.root}/test/fixtures/files/fair_data_station/seek-fair-data-station-test-case.ttl"
+    inv = Seek::FairDataStation::Reader.new.parse_graph(path).first
+    contributor = FactoryBot.create(:person)
+    projects = contributor.projects
+    policy = Policy.default
+
+    investigation = Seek::FairDataStation::Writer.new.construct_isa(inv, contributor, projects, policy)
+    assert investigation.valid?
+
+    # setup
+    assert_difference('ExtendedMetadata.count', 12) do
+      User.with_current_user(contributor.user) do
+        investigation.save!
+      end
+    end
+
+    path = "#{Rails.root}/test/fixtures/files/fair_data_station/seek-fair-data-station-modified-test-case.ttl"
+    inv = Seek::FairDataStation::Reader.new.parse_graph(path).first
+
+    # on save check, 0 investigation created, 1 study created, 1 obs unit, 1 sample, 1 assay, 3 data file, 3 extended metadata
+
+    assert_no_difference('Investigation.count') do
+      assert_difference('Study.count', 1) do
+        assert_difference('ObservationUnit.count', 1) do
+          assert_difference('Sample.count', 1) do
+            assert_difference('Assay.count', 1) do
+              assert_difference('DataFile.count', 3) do
+                assert_difference('ObservationUnitAsset.count', 1) do
+                  assert_difference('AssayAsset.count', 2) do
+                    # 1 for new df, the other is for the sample
+                    assert_difference('ExtendedMetadata.count', 3) do
+                      User.with_current_user(contributor.user) do
+                        investigation = Seek::FairDataStation::Writer.new.update_isa(investigation, inv, contributor,
+                                                                                     projects, policy)
+                        investigation.save!
+                      end
+                    end
+                  end
+                end
+              end
+            end
+          end
+        end
+      end
+    end
+
+    investigation.reload
+
+    assert_equal 3, investigation.studies.count
+    study = investigation.studies.where(external_identifier: 'seek-test-study-1').first
+    expected = HashWithIndifferentAccess.new({
+                                               'Experimental site name': 'manchester test site - changed',
+                                               'study date details': {
+                                                 'End date of Study': '2024-08-08',
+                                                 'Start date of Study': '2024-08-01'
+                                               }
+                                             })
+    assert_equal expected, study.extended_metadata.data
+
+    study = investigation.studies.where(external_identifier: 'seek-test-study-3').first
+    expected = HashWithIndifferentAccess.new({
+                                               'Experimental site name': 'birmingham-test-site',
+                                               'study date details': {
+                                                 'End date of Study': '2024-09-13',
+                                                 'Start date of Study': '2024-09-12'
+                                               }
+                                             })
+    assert_equal expected, study.extended_metadata.data
+
+    obs_unit = ObservationUnit.where(external_identifier: 'seek-test-obs-unit-1').first
+    expected = HashWithIndifferentAccess.new({
+                                               'Gender': 'female',
+                                               'obs_unit_birth_details': {
+                                                 'Birth weight': '1234g',
+                                                 'Date of birth': '2020-01-10'
+                                               }
+                                             })
+    assert_equal expected, obs_unit.extended_metadata.data
+    obs_unit = ObservationUnit.where(external_identifier: 'seek-test-obs-unit-4').first
+    expected = HashWithIndifferentAccess.new({
+                                               'Gender': 'female',
+                                               'obs_unit_birth_details': {
+                                                 'Birth weight': '1005g',
+                                                 'Date of birth': '2020-02-12'
+                                               }
+                                             })
+    assert_equal expected, obs_unit.extended_metadata.data
+
+  end
+
   private
 
   def setup_test_case_investigation