When are beneficial owners filed for a new Cyprus company, and is there a fee?

A new company files its beneficial owners within 90 days of registration, and there is no filing fee. Later changes in ownership also have to be reported within a short deadline, 45 days according to the Registrar's guidance (confirm with your specialist). Filing is done online in the beneficial ownership system.

Source: UBO register: practical implementation, Department of Registrar of Companies and Intellectual Property