Supporting smallholders’ livelihoods in fragile and biodiversity rich regions such as rainforests is a priority of many development agencies and national governments. These regions tend to be characterized by recent settlements, increasing population and infrastructure, as well as land use competing activities that put pressure upon fragile ecosystems. Research aimed at improving livelihood strategies often focuses on increasing yields and productivity, but fails to account for alternative measures such as improving agricultural practices, changing land use or improving commercialization. This paper uses household types defined according to different land use patterns in the northern Amazon region of Ecuador to explore limitations and identify future options for improving livelihood strategies based in the small-scale production of coffee and cocoa. Results for application to four types are discussed, which highlight the utility of the method and identify trade-offs in terms of environmental and social goals versus profitability. Lessons are drawn that can inform public policies oriented to improving livelihood strategies of small producers of coffee and cocoa in the Amazon region without compromising the environment.