This paper provides a customized optimization approach for the long-term audit staff scheduling problem of aviation approved training organizations (ATO) in Brazil. We formulate the problem as a set covering problem by considering both auditors’ assignments and ATO’s arrangements to minimize the total cost of staff traveling. However, the developed formulation is difficult to solve for real-world instances due to the exponential number of decision variables. Further, the formulation is inflexible enough to incorporate peculiarities of each real-world problem. Towards decreasing the problem complexity, allowing to incorporate several real features, a two-phase method is proposed. First, we group the companies to be audited in fewer groups as possible, generating fewer travels. Second, we assign auditors to the groupings of companies generated. A case study is conducted with real data from the Brazilian Civil Aviation Authority regarding audits conducted on aviation organizations. The results show the model can be used during the planning phase of audits, including scenario analysis with different parameters to support decision-makers.