Coffee cooperatives employ certification systems, in part, to structure their relations with growers and buyers, and generate income for business operations and investments. In Central America, development agencies have targeted certified coffee cooperatives for support, based on the assumption that cooperatives are uniquely positioned to deliver benefits to poor coffee farmers. Research on certification systems has focused on the benefits obtained by smallholders from participation in a single system, often Fairtrade. This research examines cooperatives and how they engage with certification systems and the implications of this engagement for building their business. Data was collected in 2018 from four cooperatives in Nicaragua and Honduras. Fairtrade certification and related coffee sales formed the bedrock of their business strategy, but Fairtrade alone was insufficient to sustain operations, even when combined with organic certification, due to insufficient demand. Additional systems, such as UTZ Certified, C.A.F.E. Practices, and Rainforest Alliance were employed. These additional systems allowed cooperatives to sell excess coffee on relatively favourable terms – coffee which otherwise would have been sold as non-certified coffee. Results suggest that engagement in multiple certification systems is critical for sustaining cooperatives in the region, but they also dampen expectations that certification systems can provide a framework for driving long-term systemic change.