In the EU budget considerable funds are earmarked for agriculture. In the Republic of Croatia, agriculture is one of the most important branches of activity. Through the Paying Agency for Agriculture, Fisheries and Rural Development, funds are invested in improving the efficiency of agricultural production and living and working conditions in rural areas. EU funds are strictly earmarked and their lawful and transparent spending should be ensured. Therefore, spending control has been introduced, both at national and European Union level, and an internal control of EU funds spending. External monitoring is carried out by a national audit, which is more based on the spending of the national budget, the Agency for the Audit of the European Union Program Implementation System (ARPA) and the European Commission audits, which are based on the work of the ARPA. This paper analyzes the procedures, laws, reports and documents that monitor the use of EU funds. A very important function in oversight is the Internal Audit Division, which, through its reports and recommendations, and, of course, by continuous monitoring, influences the improvement of the business processes of the Paying Agency for Agriculture, Fisheries and Rural Development. There is almost no room for error, since funds must be strictly channeled into the production processes for which they are intended. The role of the Internal Audit Division, which is more advisory, contributes to eliminating potential errors in business processes and contributes to improving the Agency's operations.