Sustainable certifications have been promoted as a means of recognizing environmental benefits and generating economic benefits from sustainable coffee production. A case study is presented from one region of Nicaragua where these benefits were evaluated and two producer organizations were supported to improve their access to sustainable certification. Biodiversity and carbon stocks were found to be more associated with smallholder vs. large-scale farms than with certification per se, but reduced use of agrochemicals and good management of water sources was strongly associated with certification. Economic performance of farmers with different certifications varied, C.A.F.E. Practice and Rainforest Alliance certified farmers had higher incomes but also higher levels of investment than conventional farmers, while organic farmers had a similar level of income to conventional producers but achieved this with a lower level of investment. Producer organizations require substantial external financial and technical support to access these certifications, which may place limitations on the spread of the benefits from sustainable certification to a majority of producers.