Can I sue a builder in Malta for poor quality work even after paying in full?

No, making full payment does not automatically waive your right to hold a contractor accountable for defective work, since under general principles of Maltese contract law found in the Civil Code, Chapter 16 of the Laws of Malta, a builder generally has an obligation to deliver work of proper quality and workmanship consistent with what was agreed, and defects that weren't immediately obvious or apparent at the time of payment can still generally be pursued as a breach of this obligation, provided you act within the applicable prescription period and haven't otherwise clearly and knowingly waived your rights regarding these specific defects. Document the specific quality issues you've discovered clearly, ideally with photos and, if the defects are significant or their cause is disputed, an independent professional assessment such as from a surveyor or another qualified contractor, since this evidence would be important in properly establishing both the existence of the defects and that they resulted from the builder's substandard work rather than some other cause. Depending on the specific nature and severity of the defects, your options could include formally requesting the original builder remedy the defects at their own cost, or if that's not achievable, seeking damages to cover the cost of proper remedial work by another contractor, and given the practical complexity of properly pursuing this kind of construction defect claim, it would be worth consulting a lawyer to assess your specific situation and the best route forward.