The design of complex health systems interventions, such as pay for performance (P4P), can be critical to determining such programmes' success. In P4P programmes, the design of financial incentives is crucial in shaping how these programmes work. However, the design of such schemes is usually homogenous across providers within a given scheme. Consequently, there is a limited understanding of the strengths and weaknesses of P4P design elements from the implementers' perspective. This study takes advantage of the unique context of Brazil, where municipalities adapted the federal incentive design, resulting in variations in incentive design across municipalities. The study aims to understand why municipalities in Brazil chose certain P4P design features, the associated challenges and the local adaptations made to address problems in scheme design. This study was a multiple case study design relying on qualitative data from 20 municipalities from two states in Northeastern Brazil. We conducted two key informant interviews with municipal-level stakeholders and focus group discussions with primary care providers. We also reviewed municipal Primary Care Access and Quality laws in each municipality. We found substantial variation in the design choices made by municipalities regarding 'who was incentivized', the 'payment size' and 'frequency'. Design choices affected relationships within municipalities and within teams. Challenges were chiefly associated with fairness relating to 'who received the incentive', 'what is incentivized' and the 'incentive size'. Adaptations were made to improve fairness, mostly in response to pressure from the healthcare workers. The significant variation in design choices across municipalities and providers' response to them highlights the importance of considering local context in the design and implementation of P4P schemes and ensuring flexibility to accommodate local preferences and emerging needs. Attention is needed to ensure that the choice of 'who is incentivized' and the 'size of incentives' are inclusive and fair and the allocation and 'use of funds' are transparent.