Do I need to register my company logo separately from my business name in Malta?

These are indeed treated as legally separate matters requiring separate protection. Registering your company name with the Malta Business Registry under the Companies Act, Chapter 386 of the Laws of Malta, primarily serves a corporate and administrative purpose, essentially reserving that specific company name for your entity within the companies register, but this registration does not itself grant you the exclusive trademark rights over that name, or any protection at all over a separate logo design, in the way that formal trademark registration under the Trademarks Act, Chapter 416 of the Laws of Malta, would. If you want proper legal protection preventing others from using a similar name or logo in trade, and the ability to take formal legal action against infringement, you would need to separately register these as trademarks with the Industrial Property Registrations Directorate (IPRD), and it's worth noting that your logo, as an original creative design, would also likely benefit from automatic copyright protection under the Copyright Act, Chapter 415 of the Laws of Malta, from the moment of its creation, quite separately from any trademark registration. Given that you have valuable brand assets in both your name and your logo, it would be worth discussing with an IP lawyer whether formally registering both as trademarks makes sense for your specific business, since the company registration alone leaves meaningful gaps in your actual legal protection.