diff --git a/lib/rmt/mirror/base.rb b/lib/rmt/mirror/base.rb
index 2b521cc00..43bb3023c 100644
--- a/lib/rmt/mirror/base.rb
+++ b/lib/rmt/mirror/base.rb
@@ -157,6 +157,7 @@ def cleanup_stale_metadata
 
   def move_files(glob:, destination:)
     FileUtils.mkpath(destination) unless Dir.exist?(destination)
+    FileUtils.rm_rf(Dir.glob(File.join(destination, '*')))
     FileUtils.mv(Dir.glob(glob), destination, force: true)
   rescue StandardError => e
     raise RMT::Mirror::Exception.new(_('Error while moving files %{glob} to %{dest}: %{error}') % {
diff --git a/package/obs/rmt-server.changes b/package/obs/rmt-server.changes
index c84e3dbf6..71fdda942 100644
--- a/package/obs/rmt-server.changes
+++ b/package/obs/rmt-server.changes
@@ -13,6 +13,7 @@ Wed Oct 30 09:01:32 UTC 2024 - Natnael Getahun <natnael.getahun@suse.com>
     * Allow SLE Micro system to access SLES repositories (bsc#1230419)
   * Skip system token rotation in read-only APIs
   * Enable RMT to handle the new dl.suse.com CDN domain (bsc#1234641)
+  * Clean up RMT metadata after repo update (bsc#1233308)
 
 -------------------------------------------------------------------
 Wed Aug 21 15:28:43 UTC 2024 - Jesús Bermúdez Velázquez <jesus.bv@suse.com>
diff --git a/spec/lib/rmt/mirror/base_spec.rb b/spec/lib/rmt/mirror/base_spec.rb
index 1add79b21..01453a459 100644
--- a/spec/lib/rmt/mirror/base_spec.rb
+++ b/spec/lib/rmt/mirror/base_spec.rb
@@ -230,6 +230,40 @@
 
       expect { base.move_files(glob: src, destination: dest) }.to raise_exception(/Error while moving files/)
     end
+
+    it 'removes existing files in the destination directory before moving' do
+      allow(Dir).to receive(:exist?).with(dest).and_return(true)
+      allow(Dir).to receive(:glob).with(File.join(dest, '*')).and_return(%w[/destination/path/file1.txt /destination/path/file2.txt])
+      allow(Dir).to receive(:glob).with(src).and_return(%w[/source/path/newfile1.txt /source/path/newfile2.txt])
+      expect(FileUtils).not_to receive(:mkpath).with(dest)
+      expect(FileUtils).to receive(:rm_rf).with(%w[/destination/path/file1.txt /destination/path/file2.txt])
+      expect(FileUtils).to receive(:mv).with(%w[/source/path/newfile1.txt /source/path/newfile2.txt], dest, force: true)
+
+      base.move_files(glob: src, destination: dest)
+    end
+
+    it 'removes existing files when destination directory is empty' do
+      allow(Dir).to receive(:exist?).with(dest).and_return(false)
+      allow(Dir).to receive(:glob).with(src).and_return(%w[/source/path/newfile1.txt /source/path/newfile2.txt])
+      allow(Dir).to receive(:glob).with(File.join(dest, '*')).and_return([])
+      expect(FileUtils).to receive(:mkpath).with(dest)
+      expect(FileUtils).to receive(:rm_rf).with([])
+      expect(FileUtils).to receive(:mv).with(%w[/source/path/newfile1.txt /source/path/newfile2.txt], dest, force: true)
+
+      base.move_files(glob: src, destination: dest)
+    end
+
+    it 'handles errors during removal of existing files' do
+      allow(Dir).to receive(:exist?).with(dest).and_return(true)
+      existing_files = ['/destination/path/file1.txt']
+
+      allow(Dir).to receive(:glob).with(File.join(dest, '*')).and_return(existing_files)
+      allow(FileUtils).to receive(:rm_rf).with(existing_files).and_raise(StandardError.new('Remove failed'))
+
+      expect do
+        base.move_files(glob: src, destination: dest)
+      end.to raise_exception(/Error while moving files/)
+    end
   end
 
   describe '#need_to_download?' do