Voluntary sustainability standards (VSS) have gained prominence in the agri-food sector as market-based tools to address environmental and social concerns in global supply chains. While third-party certifications like Rainforest Alliance and Fairtrade have been extensively studied, company-led in-house certifications, such as Starbucks’ C.A.F.E. Practices, remain underexplored. This paper examines the effects of in-house and third-party certifications on coffee farmers’ economic and ecological outcomes in Rwanda. Using survey data from 842 coffee farmers and ecological data from a subsample of 99 farmers, we explore the association between certifications and coffee revenues, costs, yields, vegetation structure, and animal diversity. Our findings indicate that third-party certifications enhance economic performance without compromising ecological conditions, whereas in-house certifications improve economic indicators at the expense of biodiversity. These findings underscore the need for policy measures that not only support the economic benefits of certification but also address potential ecological trade-offs, ensuring that sustainable development strategies benefit both farmers and the environment.