The marketing of coffee through group-based, certified market channels is often promoted by governments and donors as a viable business model for poor small-scale farmers. Organic and fairtrade coffees have become very popular among socially, environmentally and health conscious consumers in recent years. While coffee certification programs have been in place for over fifteen years, there are few studies on the welfare impacts of certification schemes. Therefore, this research seeks to analyse the impacts of certification on poverty alleviation and to identify the critical factors which explain success or failure of certification schemes. We use a combination of qualitative and quantitative research, comparing small-scale coffee producers in northern Nicaragua who are organized in conventional, organic, and organic-fairtrade certified cooperatives. Our results indicate that certification schemes have a low impact on poverty, including the aspect of food security. Reasons are seen in low yield levels, indebtedness, lack of entrepreneurial skills as well as cooperatives’ management capacities. We conclude that unfair trading conditions are not the main cause of poverty among smallholder coffee growers in Nicaragua. Thus, policies and projects need to address entrepreneurial skills of farmers and cooperative managers as well as amplify extension services.