diff --git a/lib/runner/strategy/poseidon.rb b/lib/runner/strategy/poseidon.rb
index 1c8ed3b9..7080ddd9 100644
--- a/lib/runner/strategy/poseidon.rb
+++ b/lib/runner/strategy/poseidon.rb
@@ -95,7 +95,10 @@ class Runner::Strategy::Poseidon < Runner::Strategy
       }
     end
     url = "#{runner_url}/files"
-    body = {copy: copy}
+
+    # First, clean the workspace and second, copy all files to their location.
+    # This ensures that no artefacts from a previous submission remain in the workspace.
+    body = {copy: copy, delete: ['./']}
     connection = Faraday.new nil, ssl: {ca_file: self.class.config[:ca_file]}
     response = connection.patch url, body.to_json, self.class.headers
     return if response.status == 204
diff --git a/spec/lib/runner/strategy/poseidon_spec.rb b/spec/lib/runner/strategy/poseidon_spec.rb
index b87bf462..f81670da 100644
--- a/spec/lib/runner/strategy/poseidon_spec.rb
+++ b/spec/lib/runner/strategy/poseidon_spec.rb
@@ -319,7 +319,7 @@ describe Runner::Strategy::Poseidon do
       WebMock
         .stub_request(:patch, "#{described_class.config[:url]}/runners/#{runner_id}/files")
         .with(
-          body: {copy: [{path: file.filepath, content: encoded_file_content}]},
+          body: {copy: [{path: file.filepath, content: encoded_file_content}], delete: ['./']},
           headers: {'Content-Type' => 'application/json'}
         )
         .to_return(body: response_body, status: response_status)