Financial assistance from the European Union is one of the major factors affecting rural development in Poland. It is therefore essential to manage EU funds at the highest level of efficiency and quality. This is dependent on many factors: the quality of legislation, the transparency of financing, the political and institutional system, the ethics of the public administration, and also the efficiency as well as the success of management verifications and audits. The last factor should be given special attention, as successful management verification is crucial to improve the protection of EU interests and expenditure of public funds, including those targeted at rural development. The Member States are responsible for protecting the EU’s financial interests and fighting fraud. The aim of this article is to present how well-designed verification systems and their solutions can help in managing Rural Development Programmes, based on the example of Poland, and how the Commission and the Member States can work closely together to protect the EU’s financial interests effectively.