diff --git a/.rubocop.yml b/.rubocop.yml
index 2c357dff0..ce367bd87 100644
--- a/.rubocop.yml
+++ b/.rubocop.yml
@@ -41,6 +41,7 @@ RSpec/MultipleExpectations:
 Metrics/ClassLength:
   Exclude:
     - lib/rmt/downloader.rb
+  Max: 250
 
 Naming/FileName:
   Exclude:
diff --git a/app/models/product.rb b/app/models/product.rb
index 8f65f7f60..91bf4d483 100644
--- a/app/models/product.rb
+++ b/app/models/product.rb
@@ -153,7 +153,7 @@ def self.recommended_extensions(root_product_ids)
     joins(:product_extensions_associations).where(products_extensions: { recommended: true, root_product_id: root_product_ids })
   end
 
-  def create_service!
+  def find_or_create_service!
     service = Service.find_by(product_id: id)
     return service if service
 
diff --git a/app/models/repository.rb b/app/models/repository.rb
index c65c602cd..64d84a3ba 100644
--- a/app/models/repository.rb
+++ b/app/models/repository.rb
@@ -18,8 +18,6 @@ class Repository < ApplicationRecord
   validates :local_path, presence: true
   validates :friendly_id, presence: true
 
-  before_destroy :ensure_destroy_possible
-
   class << self
 
     def remove_suse_repos_without_tokens!
@@ -70,10 +68,4 @@ def custom?
     scc_id.nil?
   end
 
-  private
-
-  def ensure_destroy_possible
-    throw(:abort) unless custom?
-  end
-
 end
diff --git a/app/services/repository_service.rb b/app/services/repository_service.rb
index d967feb7b..7f5ebe7ca 100644
--- a/app/services/repository_service.rb
+++ b/app/services/repository_service.rb
@@ -3,7 +3,7 @@ class RepositoryService
   class RepositoryNotFound < RuntimeError
   end
 
-  def create_repository!(product, url, attributes, custom: false)
+  def update_or_create_repository!(product, url, attributes, custom: false)
     repository = if custom
                    Repository.find_or_initialize_by(external_url: url)
                  else
diff --git a/engines/scc_proxy/lib/scc_proxy/engine.rb b/engines/scc_proxy/lib/scc_proxy/engine.rb
index 2d57185f9..93a48775a 100644
--- a/engines/scc_proxy/lib/scc_proxy/engine.rb
+++ b/engines/scc_proxy/lib/scc_proxy/engine.rb
@@ -283,7 +283,6 @@ def scc_upgrade(auth, product, system_login, mode, logger)
     end
   end
 
-  # rubocop:disable Metrics/ClassLength
   class Engine < ::Rails::Engine
     isolate_namespace SccProxy
     config.generators.api_only = true
@@ -523,6 +522,5 @@ def get_system(systems)
       end
     end
   end
-  # rubocop:enable Metrics/ClassLength
 end
 # rubocop:enable Metrics/ModuleLength
diff --git a/lib/rmt/cli/repos_custom.rb b/lib/rmt/cli/repos_custom.rb
index cccf333ea..482626fe1 100644
--- a/lib/rmt/cli/repos_custom.rb
+++ b/lib/rmt/cli/repos_custom.rb
@@ -35,7 +35,7 @@ def add(url, name)
       raise RMT::CLI::Error.new(_("Couldn't add custom repository."))
     end
 
-    repository_service.create_repository!(nil, url, {
+    repository_service.update_or_create_repository!(nil, url, {
       name: name.strip,
       mirroring_enabled: true,
       autorefresh: true,
diff --git a/lib/rmt/scc.rb b/lib/rmt/scc.rb
index 59fccdf2a..8e50fc145 100644
--- a/lib/rmt/scc.rb
+++ b/lib/rmt/scc.rb
@@ -23,13 +23,32 @@ def sync
     data.each { |item| create_product(item) }
     data.each { |item| migration_paths(item) }
 
-    update_repositories(scc_api_client.list_repositories)
+    # Update repositories with details (eg. access token) from API
+    repositories_data = scc_api_client.list_repositories
+    update_repositories(repositories_data)
 
     Repository.remove_suse_repos_without_tokens!
+    remove_obsolete_repositories(repositories_data)
 
     update_subscriptions(scc_api_client.list_subscriptions)
   end
 
+  def remove_obsolete_repositories(repos_data)
+    @logger.info _('Removing obsolete repositories')
+    return if repos_data.empty?
+
+    scc_repo_ids = repos_data.pluck(:id)
+
+
+    # Find repositories in RMT that no longer exist in SCC
+    # Only consider repositories that have a non-null scc_id
+    repos_to_remove = Repository.only_scc.where.not(scc_id: scc_repo_ids)
+    if repos_to_remove.any?
+      repos_to_remove.destroy_all
+      @logger.debug("Successfully removed #{repos_to_remove.count} obsolete repositories")
+    end
+  end
+
   def export(path)
     credentials_set? || (raise CredentialsError, 'SCC credentials not set.')
 
@@ -185,10 +204,21 @@ def create_product(item, root_product_id = nil, base_product = nil, recommended
   end
 
   def create_service(item, product)
-    product.create_service!
+    service = product.find_or_create_service!
+
     item[:repositories].each do |repo_item|
-      repository_service.create_repository!(product, repo_item[:url], repo_item)
+      repository_service.update_or_create_repository!(product, repo_item[:url], repo_item)
     end
+
+    # detect repositories removed from the product in SCC
+    removed_repos = service.repositories.only_scc.where.not(scc_id: item[:repositories].pluck(:id))
+    disassociate_repositories(service, removed_repos) if removed_repos.present?
+
+  end
+
+  def disassociate_repositories(service, repos)
+    service.repositories.delete(repos)
+    @logger.debug("Removed repositories #{repos.pluck(:scc_id)} from '#{service.product.friendly_name}'")
   end
 
   def migration_paths(item)
diff --git a/package/obs/rmt-server.changes b/package/obs/rmt-server.changes
index 0fe7923d6..5678987df 100644
--- a/package/obs/rmt-server.changes
+++ b/package/obs/rmt-server.changes
@@ -7,6 +7,7 @@ Mon Dec 23 14:07:00 UTC 2024 - Luís Caparroz <lcaparroz@suse.com>
   * rmt-server-pubcloud:
     * Update Micro check due to Micro 6.0 and 6.1 identifier to keep bsc#1230419 in place
     * Update Zypper path allowing check to handle paid extensions (i.e. LTSS) (bsc#1230157)
+  * Remove obsolete repositories and associations from rmt during SCC sync (bsc#1232808)
 
 -------------------------------------------------------------------
 Mon Dec 23 08:03:56 UTC 2024 - Parag Jain <parag.jain@suse.com>
diff --git a/spec/factories/products.rb b/spec/factories/products.rb
index 4612dfb00..8e2120740 100644
--- a/spec/factories/products.rb
+++ b/spec/factories/products.rb
@@ -117,7 +117,7 @@
 
     trait :with_service do
       after :create do |product, _evaluator|
-        product.create_service!
+        product.find_or_create_service!
       end
     end
 
diff --git a/spec/factories/services.rb b/spec/factories/services.rb
index fe74e26ae..f7902653c 100644
--- a/spec/factories/services.rb
+++ b/spec/factories/services.rb
@@ -66,3 +66,10 @@
     end
   end
 end
+
+FactoryBot.define do
+  factory :repositories_services_association do
+    association :repository
+    association :service
+  end
+end
diff --git a/spec/lib/rmt/scc_spec.rb b/spec/lib/rmt/scc_spec.rb
index f1e3b9d61..6bdec095c 100644
--- a/spec/lib/rmt/scc_spec.rb
+++ b/spec/lib/rmt/scc_spec.rb
@@ -247,7 +247,7 @@
 
   describe '#remove_suse_repos_without_tokens' do
     let(:api_double) { double }
-    let!(:suse_repo_with_token) { FactoryBot.create(:repository, :with_products, auth_token: 'auth_token') }
+    let!(:suse_repo_with_token) { FactoryBot.create(:repository, :with_products, auth_token: 'auth_token', scc_id: 200000) }
     let!(:suse_repo_without_token) do
       FactoryBot.create(
         :repository,
@@ -262,7 +262,8 @@
         :with_products,
         auth_token: nil,
         external_url: 'https://installer-updates.suse.com/repos/not/updates',
-        installer_updates: true
+        installer_updates: true,
+        scc_id: 200001
       )
     end
     let!(:custom_repo) do
@@ -314,6 +315,119 @@ def scc
     end
   end
 
+  describe '#remove_obsolete_repositories' do
+    let(:api_double) { instance_double 'SUSE::Connect::Api' }
+    let(:logger) { instance_double('RMT::Logger').as_null_object }
+    let!(:suse_repo_one) { create(:repository, :with_products, scc_id: 1) }
+    let!(:suse_repo_two) { create(:repository, :with_products, scc_id: 2) }
+    let!(:custom_repo) { create(:repository, :with_products, scc_id: nil) }
+
+    before do
+      allow(Settings).to receive(:scc).and_return OpenStruct.new(username: 'foo', password: 'bar')
+      allow(RMT::Logger).to receive(:new).and_return(logger)
+    end
+
+    context 'when repos_data is empty' do
+      it 'returns early and does not remove any repositories' do
+        expect(Repository).not_to receive(:only_scc)
+        described_class.new.remove_obsolete_repositories([])
+        expect(Repository.count).to eq(3)
+      end
+    end
+
+    context 'when repos_data contains all existing SCC repositories' do
+      let(:repos_data) do
+        [
+          { id: suse_repo_one.scc_id },
+          { id: suse_repo_two.scc_id }
+        ]
+      end
+
+      it 'does not remove any repositories' do
+        expect { described_class.new.remove_obsolete_repositories(repos_data) }.not_to change(Repository, :count)
+      end
+    end
+
+    context 'when repos_data is missing some existing SCC repositories' do
+      let(:repos_data) do
+        [
+          { id: suse_repo_one.scc_id }
+        ]
+      end
+
+      it 'removes only the obsolete SCC repositories' do
+        expect { described_class.new.remove_obsolete_repositories(repos_data) }.to change(Repository, :count).by(-1)
+
+        expect(Repository.find_by(id: suse_repo_one.id)).to be_present
+        expect(Repository.find_by(id: suse_repo_two.id)).to be_nil
+        expect(Repository.find_by(id: custom_repo.id)).to be_present
+      end
+    end
+
+    context 'when repos_data does not contain any existing SCC repository IDs' do
+      let(:repos_data) do
+        [
+          { id: 999 }
+        ]
+      end
+
+      it 'removes all SCC repositories' do
+        expect { described_class.new.remove_obsolete_repositories(repos_data) }.to change(Repository, :count).by(-2)
+
+        expect(Repository.find_by(id: suse_repo_one.id)).to be_nil
+        expect(Repository.find_by(id: suse_repo_two.id)).to be_nil
+        expect(Repository.find_by(id: custom_repo.id)).to be_present
+      end
+    end
+  end
+
+
+  describe '#disassociate_repositories' do
+    let(:logger) { instance_double('RMT::Logger').as_null_object }
+    let(:product) { create(:product) }
+    let(:service) { create(:service, product: product) }
+
+    before do
+      allow(RMT::Logger).to receive(:new).and_return(logger)
+    end
+
+    context 'when existing_repo_ids is empty' do
+      it 'does not remove any associations' do
+        expect { described_class.new.send(:disassociate_repositories, service, []) }.not_to change(RepositoriesServicesAssociation, :count)
+      end
+    end
+
+    context 'when existing_repo_ids contains repository IDs' do
+      let!(:repo_one) { create(:repository, :with_products, scc_id: 101) }
+      let!(:repo_two) { create(:repository, :with_products, scc_id: 102) }
+      let!(:repo_three) { create(:repository, :with_products, scc_id: 103) }
+      let(:existing_repo_ids) { [repo_one.scc_id, repo_two.scc_id] }
+
+      before do
+        # Associate repositories with the product through services
+        [repo_one, repo_two, repo_three].each do |repo|
+          create(:repositories_services_association,
+                 repository: repo,
+                 service: service)
+        end
+      end
+
+      it 'removes repository associations for the specified repo IDs' do
+        expect do
+          described_class.new.send(:disassociate_repositories, service, [repo_one, repo_two])
+        end.to change(RepositoriesServicesAssociation, :count).by(-2)
+      end
+
+      it 'only removes associations for specified repositories' do
+        described_class.new.send(:disassociate_repositories, service, [repo_one, repo_two])
+
+        expect(product.repositories).not_to include(repo_one)
+        expect(product.repositories).not_to include(repo_two)
+        expect(product.repositories).to include(repo_three)
+      end
+    end
+  end
+
   describe '#export' do
     let(:path) { '/tmp/usb' }
 
diff --git a/spec/models/product_spec.rb b/spec/models/product_spec.rb
index 5dc3771b3..56dea3964 100644
--- a/spec/models/product_spec.rb
+++ b/spec/models/product_spec.rb
@@ -218,13 +218,13 @@
     end
   end
 
-  describe '#create_service!' do
+  describe '#find_or_create_service!' do
     context 'when service already exists' do
       let!(:product) { create :product }
       let!(:service) { create :service, product_id: product.id }
 
       it 'returns the existing service' do
-        expect(product.create_service!).to eq(service)
+        expect(product.find_or_create_service!).to eq(service)
       end
     end
 
@@ -234,7 +234,7 @@
       let!(:other_service) { create :service, id: product.id, product_id: other_product.id }
 
       it 'creates a service with a random ID' do
-        expect(product.create_service!.id).not_to eq(other_service.id)
+        expect(product.find_or_create_service!.id).not_to eq(other_service.id)
       end
     end
 
@@ -242,7 +242,7 @@
       let!(:product) { create :product }
 
       it 'creates a service with a matching ID' do
-        expect(product.create_service!.id).to eq(product.id)
+        expect(product.find_or_create_service!.id).to eq(product.id)
       end
     end
   end
diff --git a/spec/models/repository_spec.rb b/spec/models/repository_spec.rb
index 3c49cd6fa..7233de218 100644
--- a/spec/models/repository_spec.rb
+++ b/spec/models/repository_spec.rb
@@ -227,14 +227,6 @@
   end
 
   describe '#destroy' do
-    context 'when it is an official repository' do
-      subject { repository.destroy }
-
-      let!(:repository) { create :repository }
-
-      it { is_expected.to be_falsey }
-    end
-
     context 'when it is a custom repository' do
       subject { repository.destroy }
 
diff --git a/spec/services/repository_service_spec.rb b/spec/services/repository_service_spec.rb
index 0035395b5..d028aa837 100644
--- a/spec/services/repository_service_spec.rb
+++ b/spec/services/repository_service_spec.rb
@@ -6,7 +6,7 @@
   let(:product) { create :product, :with_service }
 
   describe '#create_repository' do
-    subject(:repository) { service.create_repository!(product, url, attributes, custom: custom).reload }
+    subject(:repository) { service.update_or_create_repository!(product, url, attributes, custom: custom).reload }
 
     let(:attributes) do
       {
@@ -38,10 +38,10 @@
 
     context 'URLs of SCC repositories changes' do
       subject(:repository) do
-        service.create_repository!(product, old_url, attributes, custom: custom)
+        service.update_or_create_repository!(product, old_url, attributes, custom: custom)
         expect(Repository.find_by(external_url: old_url)).not_to eq(nil)
 
-        service.create_repository!(product, url, attributes, custom: custom).reload
+        service.update_or_create_repository!(product, url, attributes, custom: custom).reload
       end
 
       let(:old_url) { 'https://foo.bar.com/bar/foo' }
@@ -53,10 +53,10 @@
 
     context 'self heals SCC repos' do
       subject(:repository) do
-        service.create_repository!(product, url, attributes, custom: custom).update(scc_id: old_scc_id)
+        service.update_or_create_repository!(product, url, attributes, custom: custom).update(scc_id: old_scc_id)
         expect(Repository.find_by(scc_id: old_scc_id)).not_to eq(nil)
 
-        service.create_repository!(product, url, attributes, custom: custom).reload
+        service.update_or_create_repository!(product, url, attributes, custom: custom).reload
       end
 
       let(:old_scc_id) { 666 }
@@ -68,8 +68,8 @@
 
     context 'custom repo with same url' do
       subject(:repository) do
-        service.create_repository!(product, url, attributes, custom: custom).update(scc_id: nil)
-        service.create_repository!(product, url, attributes, custom: custom).reload
+        service.update_or_create_repository!(product, url, attributes, custom: custom).update(scc_id: nil)
+        service.update_or_create_repository!(product, url, attributes, custom: custom).reload
       end
 
       it_behaves_like 'scc repositories'
@@ -90,9 +90,9 @@
 
       context 'already existing repositories with changing URL', :skip_sqlite do
         subject(:repository) do
-          service.create_repository!(product, url, attributes, custom: custom).reload
+          service.update_or_create_repository!(product, url, attributes, custom: custom).reload
           url = 'https://foo.bar.com/bar/foo'
-          service.create_repository!(product, url, attributes, custom: custom).reload
+          service.update_or_create_repository!(product, url, attributes, custom: custom).reload
         end
 
         it('raises error when the id is the same') { expect { repository }.to raise_error(/Duplicate entry/) }