diff --git a/app/controllers/assays_controller.rb b/app/controllers/assays_controller.rb
index 66236dd6c9..0c88fabba4 100644
--- a/app/controllers/assays_controller.rb
+++ b/app/controllers/assays_controller.rb
@@ -1,16 +1,17 @@
 class AssaysController < ApplicationController
-
   include Seek::IndexPager
   include Seek::AssetsCommon
 
   before_action :assays_enabled?
-  before_action :find_assets, :only=>[:index]
-  before_action :find_and_authorize_requested_item, :only=>[:edit, :update, :destroy, :manage, :manage_update, :show, :new_object_based_on_existing_one]
+  before_action :find_assets, only: [:index]
+  before_action :find_and_authorize_requested_item,
+                only: %i[edit update destroy manage manage_update show new_object_based_on_existing_one]
+  before_action :fix_assay_linkage, only: [:destroy]
   before_action :delete_linked_sample_types, only: [:destroy]
 
-  #project_membership_required_appended is an alias to project_membership_required, but is necessary to include the actions
-  #defined in the application controller
-  before_action :project_membership_required_appended, :only=>[:new_object_based_on_existing_one]
+  # project_membership_required_appended is an alias to project_membership_required, but is necessary to include the actions
+  # defined in the application controller
+  before_action :project_membership_required_appended, only: [:new_object_based_on_existing_one]
 
   include Seek::Publishing::PublishingCommon
 
@@ -30,69 +31,63 @@ def new_object_based_on_existing_one
       end
 
       @existing_assay.data_files.each do |d|
-        if !d.can_view?
+        unless d.can_view?
           notice_message << "Some or all #{t('data_file').pluralize} of the existing #{t('assays.assay')} cannot be viewed, you may specify your own! <br/>"
           break
         end
       end
       @existing_assay.sops.each do |s|
-        if !s.can_view?
-          notice_message << "Some or all #{t('sop').pluralize} of the existing #{ t('assays.assay')} cannot be viewed, you may specify your own! <br/>"
+        unless s.can_view?
+          notice_message << "Some or all #{t('sop').pluralize} of the existing #{t('assays.assay')} cannot be viewed, you may specify your own! <br/>"
           break
         end
       end
       @existing_assay.models.each do |m|
-        if !m.can_view?
+        unless m.can_view?
           notice_message << "Some or all #{t('model').pluralize} of the existing #{t('assays.assay')} cannot be viewed, you may specify your own! <br/>"
           break
         end
       end
       @existing_assay.documents.each do |d|
-        if !d.can_view?
+        unless d.can_view?
           notice_message << "Some or all #{t('document').pluralize} of the existing #{t('assays.assay')} cannot be viewed, you may specify your own! <br/>"
           break
         end
       end
 
-      unless notice_message.blank?
-        flash.now[:notice] = notice_message.html_safe
-      end
+      flash.now[:notice] = notice_message.html_safe unless notice_message.blank?
 
-      render :action=>"new"
+      render action: 'new'
     else
-      flash[:error]="You do not have the necessary permissions to copy this #{t('assays.assay')}"
+      flash[:error] = "You do not have the necessary permissions to copy this #{t('assays.assay')}"
       redirect_to @existing_assay
     end
   end
 
   def new
-    @assay=setup_new_asset
-    @assay_class=params[:class]
+    @assay = setup_new_asset
+    @assay_class = params[:class]
     @permitted_params = assay_params if params[:assay]
 
-    #jump straight to experimental if modelling analysis is disabled
-    @assay_class ||= "experimental" unless Seek::Config.modelling_analysis_enabled
+    # jump straight to experimental if modelling analysis is disabled
+    @assay_class ||= 'experimental' unless Seek::Config.modelling_analysis_enabled
 
-    @assay.assay_class=AssayClass.for_type(@assay_class) unless @assay_class.nil?
+    @assay.assay_class = AssayClass.for_type(@assay_class) unless @assay_class.nil?
 
-    respond_to do |format|
-      format.html
-    end
+    respond_to(&:html)
   end
 
   def edit
-    respond_to do |format|
-      format.html
-    end
+    respond_to(&:html)
   end
 
   def create
-    params[:assay_class_id] ||= AssayClass.for_type("experimental").id
+    params[:assay_class_id] ||= AssayClass.for_type('experimental').id
     @assay = Assay.new(assay_params)
 
     update_assay_organisms @assay, params
     update_assay_human_diseases @assay, params
-    @assay.contributor=current_person
+    @assay.contributor = current_person
     update_sharing_policies @assay
     update_annotations(params[:tag_list], @assay)
     update_relationships(@assay, params)
@@ -101,17 +96,16 @@ def create
       respond_to do |format|
         flash[:notice] = "#{t('assays.assay')} was successfully created."
         format.html { redirect_to(@assay) }
-        format.json {render json: @assay, include: [params[:include]]}
+        format.json { render json: @assay, include: [params[:include]] }
       end
     else
       respond_to do |format|
-        format.html { render :action => "new", status: :unprocessable_entity }
+        format.html { render action: 'new', status: :unprocessable_entity }
         format.json { render json: json_api_errors(@assay), status: :unprocessable_entity }
       end
     end
   end
 
-
   def delete_linked_sample_types
     return unless is_single_page_assay?
     return if @assay.sample_type.nil?
@@ -119,6 +113,23 @@ def delete_linked_sample_types
     @assay.sample_type.destroy
   end
 
+  def fix_assay_linkage
+    return unless is_single_page_assay?
+    return unless @assay.has_linked_child_assay?
+
+    previous_assay_linked_st_id = @assay.previous_linked_assay_sample_type&.id
+
+    next_assay = Assay.all.detect do |a|
+      a.sample_type&.sample_attributes&.first&.linked_sample_type_id == @assay.sample_type_id
+    end
+
+    next_assay_st_attr = next_assay.sample_type&.sample_attributes&.first
+
+    return unless next_assay && previous_assay_linked_st_id && next_assay_st_attr
+
+    next_assay_st_attr.update(linked_sample_type_id: previous_assay_linked_st_id)
+  end
+
   def update
     update_assay_organisms @assay, params
     update_assay_human_diseases @assay, params
@@ -130,26 +141,26 @@ def update
       if @assay.update(assay_params)
         flash[:notice] = "#{t('assays.assay')} was successfully updated."
         format.html { redirect_to(@assay) }
-        format.json {render json: @assay, include: [params[:include]]}
+        format.json { render json: @assay, include: [params[:include]] }
       else
-        format.html { render :action => "edit", status: :unprocessable_entity }
+        format.html { render action: 'edit', status: :unprocessable_entity }
         format.json { render json: json_api_errors(@assay), status: :unprocessable_entity }
       end
     end
   end
 
-  def update_assay_organisms assay,params
+  def update_assay_organisms(assay, params)
     organisms             = params[:assay_organism_ids] || params[:assay][:organism_ids] || []
     assay.assay_organisms = [] # This means new AssayOrganisms are created every time the assay is updated!
     Array(organisms).each do |text|
       # TODO: Refactor this to use proper nested params:
-      o_id, strain,strain_id,culture_growth_type_text,t_id,t_title=text.split(",")
-      culture_growth=CultureGrowthType.find_by_title(culture_growth_type_text)
-      assay.associate_organism(o_id, strain_id, culture_growth,t_id,t_title)
+      o_id, strain, strain_id, culture_growth_type_text, t_id, t_title = text.split(',')
+      culture_growth = CultureGrowthType.find_by_title(culture_growth_type_text)
+      assay.associate_organism(o_id, strain_id, culture_growth, t_id, t_title)
     end
   end
 
-  def update_assay_human_diseases assay,params
+  def update_assay_human_diseases(assay, params)
     human_diseases             = params[:assay_human_disease_ids] || params[:assay][:human_disease_ids] || []
     assay.assay_human_diseases = []
     Array(human_diseases).each do |human_disease_id|
@@ -159,10 +170,9 @@ def update_assay_human_diseases assay,params
 
   def show
     respond_to do |format|
-      format.html { render(params[:only_content] ? { layout: false } : {})}
-      format.rdf { render :template=>'rdf/show'}
-      format.json {render json: @assay, include: [params[:include]]}
-
+      format.html { render(params[:only_content] ? { layout: false } : {}) }
+      format.rdf { render template: 'rdf/show' }
+      format.json { render json: @assay, include: [params[:include]] }
     end
   end
 
@@ -170,11 +180,11 @@ def show
 
   def assay_params
     params.require(:assay).permit(:title, :description, :study_id, :assay_class_id, :assay_type_uri, :technology_type_uri,
-                                  :license, *creator_related_params, :position, { document_ids: []},
+                                  :license, *creator_related_params, :position, { document_ids: [] },
                                   { sop_ids: [] }, { model_ids: [] },
-                                  { samples_attributes: [:asset_id, :direction] },
-                                  { data_files_attributes: [:asset_id, :direction, :relationship_type_id] },
-                                  { placeholders_attributes: [:asset_id, :direction, :relationship_type_id] },
+                                  { samples_attributes: %i[asset_id direction] },
+                                  { data_files_attributes: %i[asset_id direction relationship_type_id] },
+                                  { placeholders_attributes: %i[asset_id direction relationship_type_id] },
                                   { publication_ids: [] },
                                   { extended_metadata_attributes: determine_extended_metadata_keys },
           { discussion_links_attributes:[:id, :url, :label, :_destroy] }
diff --git a/app/models/assay.rb b/app/models/assay.rb
index 13b2b9279e..11805ed5d8 100644
--- a/app/models/assay.rb
+++ b/app/models/assay.rb
@@ -1,10 +1,9 @@
 class Assay < ApplicationRecord
-
   include Seek::Ontologies::AssayOntologyTypes
 
-  enum status: [:planned, :running, :completed, :cancelled, :failed]
+  enum status: %i[planned running completed cancelled failed]
   belongs_to :assignee, class_name: 'Person'
-  
+
   # needs to before acts_as_isa - otherwise auto_index=>false is overridden by Seek::Search::CommonFields
   if Seek::Config.solr_enabled
     searchable(auto_index: false) do
@@ -24,7 +23,7 @@ class Assay < ApplicationRecord
   acts_as_isa
   acts_as_snapshottable
 
-  belongs_to :sample_type 
+  belongs_to :sample_type
 
   belongs_to :assay_class
   has_many :assay_organisms, dependent: :destroy, inverse_of: :assay
@@ -49,9 +48,9 @@ class Assay < ApplicationRecord
   has_one :investigation, through: :study
   has_one :external_asset, as: :seek_entity, dependent: :destroy
 
-  validates :assay_type_uri, presence:true
+  validates :assay_type_uri, presence: true
   validates_with AssayTypeUriValidator
-  validates :technology_type_uri, absence:true, if: :is_modelling?
+  validates :technology_type_uri, absence: true, if: :is_modelling?
   validates_with TechnologyTypeUriValidator
   validates_presence_of :contributor
   validates_presence_of :assay_class
@@ -66,6 +65,14 @@ class Assay < ApplicationRecord
 
   enforce_authorization_on_association :study, :view
 
+  def previous_linked_assay_sample_type
+    sample_type.sample_attributes.detect { |sa| sa.isa_tag.nil? && sa.title.include?('Input') }&.linked_sample_type
+  end
+
+  def has_linked_child_assay?
+    sample_type&.linked_sample_attributes&.any?
+  end
+
   def default_contributor
     User.current_user.try :person
   end
@@ -91,7 +98,7 @@ def is_experimental?
   end
 
   def associated_samples_through_sample_type
-    (sample_type.nil? || sample_type.samples.nil?) ? [] : sample_type.samples
+    sample_type.nil? || sample_type.samples.nil? ? [] : sample_type.samples
   end
 
   # Create or update relationship of this assay to another, with a specific relationship type and version
@@ -103,9 +110,7 @@ def associate(asset, options = {})
     else
       assay_asset = assay_assets.detect { |aa| aa.asset == asset }
 
-      if assay_asset.nil?
-        assay_asset = assay_assets.build
-      end
+      assay_asset = assay_assets.build if assay_asset.nil?
 
       assay_asset.asset = asset
       assay_asset.version = asset.version if asset && asset.respond_to?(:version)
@@ -124,12 +129,12 @@ def associate(asset, options = {})
   end
 
   def self.simple_associated_asset_types
-    [:models, :sops, :publications, :documents]
+    %i[models sops publications documents]
   end
 
   # Associations where there is additional metadata on the association, i.e. `direction`
   def self.complex_associated_asset_types
-    [:data_files, :samples, :placeholders]
+    %i[data_files samples placeholders]
   end
 
   def assets
@@ -166,7 +171,9 @@ def avatar_key
   def clone_with_associations
     new_object = dup
     new_object.policy = policy.deep_copy
-    new_object.assay_assets = assay_assets.select { |aa| self.class.complex_associated_asset_types.include?(aa.asset_type.underscore.pluralize.to_sym) }.map(&:dup)
+    new_object.assay_assets = assay_assets.select do |aa|
+      self.class.complex_associated_asset_types.include?(aa.asset_type.underscore.pluralize.to_sym)
+    end.map(&:dup)
     self.class.simple_associated_asset_types.each do |type|
       new_object.send("#{type}=", try(type))
     end
@@ -187,7 +194,8 @@ def human_disease_terms
   # organism may be either an ID or Organism instance
   # strain_id should be the id of the strain
   # culture_growth should be the culture growth instance
-  def associate_organism(organism, strain_id = nil, culture_growth_type = nil, tissue_and_cell_type_id = nil, tissue_and_cell_type_title = nil)
+  def associate_organism(organism, strain_id = nil, culture_growth_type = nil, tissue_and_cell_type_id = nil,
+                         tissue_and_cell_type_title = nil)
     organism = Organism.find(organism) if organism.is_a?(Numeric) || organism.is_a?(String)
     strain = organism.strains.find_by_id(strain_id)
     tissue_and_cell_type = nil
@@ -197,22 +205,22 @@ def associate_organism(organism, strain_id = nil, culture_growth_type = nil, tis
       tissue_and_cell_type = TissueAndCellType.where(title: tissue_and_cell_type_title).first_or_create!
     end
 
-    unless AssayOrganism.exists_for?(self, organism, strain, culture_growth_type, tissue_and_cell_type)
-      assay_organism = AssayOrganism.new(assay: self, organism: organism, culture_growth_type: culture_growth_type,
-                                         strain: strain, tissue_and_cell_type: tissue_and_cell_type)
-      assay_organisms << assay_organism
-    end
+    return if AssayOrganism.exists_for?(self, organism, strain, culture_growth_type, tissue_and_cell_type)
+
+    assay_organism = AssayOrganism.new(assay: self, organism:, culture_growth_type:,
+                                       strain:, tissue_and_cell_type:)
+    assay_organisms << assay_organism
   end
 
   # Associates a human disease with the assay
   # human disease may be either an ID or HumanDisease instance
   def associate_human_disease(human_disease)
     human_disease = HumanDisease.find(human_disease) if human_disease.is_a?(Numeric) || human_disease.is_a?(String)
-    assay_human_disease = AssayHumanDisease.new(assay: self, human_disease: human_disease)
+    assay_human_disease = AssayHumanDisease.new(assay: self, human_disease:)
 
-    unless AssayHumanDisease.exists_for?(human_disease, self)
-      assay_human_diseases << assay_human_disease
-    end
+    return if AssayHumanDisease.exists_for?(human_disease, self)
+
+    assay_human_diseases << assay_human_disease
   end
 
   # overides that from Seek::RDF::RdfGeneration, as Assay entity depends upon the AssayClass (modelling, or experimental) of the Assay
@@ -224,15 +232,15 @@ def external_asset_search_terms
     external_asset ? external_asset.search_terms : []
   end
 
-  def samples_attributes= attributes
+  def samples_attributes=(attributes)
     set_assay_assets_for('Sample', attributes)
   end
 
-  def data_files_attributes= attributes
+  def data_files_attributes=(attributes)
     set_assay_assets_for('DataFile', attributes)
   end
 
-  def placeholders_attributes= attributes
+  def placeholders_attributes=(attributes)
     set_assay_assets_for('Placeholder', attributes)
   end
 
@@ -243,7 +251,7 @@ def self.filter_by_projects(projects)
   private
 
   def set_assay_assets_for(type, attributes)
-    type_assay_assets, other_assay_assets = self.assay_assets.partition { |aa| aa.asset_type == type }
+    type_assay_assets, other_assay_assets = assay_assets.partition { |aa| aa.asset_type == type }
     new_type_assay_assets = []
 
     attributes.each do |attrs|
@@ -252,15 +260,13 @@ def set_assay_assets_for(type, attributes)
       if existing
         new_type_assay_assets << existing.tap { |e| e.assign_attributes(attrs) }
       else
-        aa = self.assay_assets.build(attrs)
-        if aa.asset && aa.asset.can_view?
-          new_type_assay_assets << aa
-        end
+        aa = assay_assets.build(attrs)
+        new_type_assay_assets << aa if aa.asset && aa.asset.can_view?
       end
     end
 
     self.assay_assets = (other_assay_assets + new_type_assay_assets)
-    self.assay_assets
+    assay_assets
   end
 
   def related_publication_ids
diff --git a/test/functional/assays_controller_test.rb b/test/functional/assays_controller_test.rb
index 968c31a910..1d05cc4a77 100644
--- a/test/functional/assays_controller_test.rb
+++ b/test/functional/assays_controller_test.rb
@@ -1923,7 +1923,12 @@ def check_fixtures_for_authorization_of_sops_and_datafiles_links
 
   test 'should delete empty assay with linked sample type' do
     person = FactoryBot.create(:person)
-    assay_sample_type = FactoryBot.create :linked_sample_type, contributor: person
+    project = person.projects.first
+    source_st = FactoryBot.create(:isa_source_sample_type, contributor: person, projects: [project])
+    sample_collection_st = FactoryBot.create(:isa_sample_collection_sample_type, contributor: person, projects: [project],
+    linked_sample_type: source_st)
+
+    assay_sample_type = FactoryBot.create :isa_assay_sample_type, linked_sample_type: sample_collection_st, contributor: person, isa_template: Template.find_by_title('ISA Assay 1')
     assay = FactoryBot.create(:assay,
                               policy:FactoryBot.create(:private_policy, permissions:[FactoryBot.create(:permission,contributor: person, access_type:Policy::EDITING)]),
                               sample_type: assay_sample_type,
@@ -1937,4 +1942,46 @@ def check_fixtures_for_authorization_of_sops_and_datafiles_links
       end
     end
   end
+
+  test 'should fix sample type linkage when middle assay is deleted' do
+    # person = User.current_user.person
+    person = FactoryBot.create(:person)
+    project = person.projects.first
+    investigation = FactoryBot.create(:investigation, projects: [project])
+
+    source_st = FactoryBot.create(:isa_source_sample_type, contributor: person, projects: [project])
+    sample_collection_st = FactoryBot.create(:isa_sample_collection_sample_type, contributor: person, projects: [project],
+                                                                                 linked_sample_type: source_st)
+
+    assay_st1 = FactoryBot.create(:isa_assay_sample_type, contributor: person, projects: [project],
+                                                          linked_sample_type: sample_collection_st, isa_template: Template.find_by_title('ISA Assay 1'))
+
+    assay_st2 = FactoryBot.create(:isa_assay_sample_type, contributor: person, projects: [project],
+                                                          linked_sample_type: assay_st1, isa_template: Template.find_by_title('ISA Assay 1'))
+
+    assay_st3 = FactoryBot.create(:isa_assay_sample_type, contributor: person, projects: [project],
+                                                          linked_sample_type: assay_st2, isa_template: Template.find_by_title('ISA Assay 1'))
+
+    study = FactoryBot.create(:study, investigation:, contributor: person,
+                                      policy: FactoryBot.create(:private_policy, permissions: [FactoryBot.create(:permission, contributor: person, access_type: Policy::MANAGING)]),
+                                      sops: [FactoryBot.create(:sop, policy: FactoryBot.create(:public_policy))],
+                                      sample_types: [source_st, sample_collection_st])
+
+    assay1 = FactoryBot.create(:assay, study:, contributor: person, sample_type: assay_st1,
+                                       policy: FactoryBot.create(:private_policy, permissions: [FactoryBot.create(:permission, contributor: person, access_type: Policy::MANAGING)]))
+    assay2 = FactoryBot.create(:assay, study:, contributor: person, sample_type: assay_st2,
+                                       policy: FactoryBot.create(:private_policy, permissions: [FactoryBot.create(:permission, contributor: person, access_type: Policy::MANAGING)]))
+    assay3 = FactoryBot.create(:assay, study:, contributor: person, sample_type: assay_st3,
+                                       policy: FactoryBot.create(:private_policy, permissions: [FactoryBot.create(:permission, contributor: person, access_type: Policy::MANAGING)]))
+
+    login_as(person)
+
+    assert_difference "Assay.count", -1 do
+      delete :destroy, params: { id: assay2.id, return_to: '/single_pages/' }
+    end
+
+    assay3.reload
+
+    assert_equal(assay3.previous_linked_assay_sample_type&.id, assay1.sample_type&.id)
+  end
 end