Despite the growing interest in Ecosystem-based Adaptation, there has been little discussion of how this approach could be used to help smallholder farmers adapt to climate change, while ensuring the continued provision of ecosystem services on which farming depends. Here we provide a framework for identifying which agricultural practices could be considered ‘Ecosystem-based Adaptation’ practices, and highlight the opportunities and constraints for using these practices to help smallholder farmers adapt to climate change. We argue that these practices are (a) based on the conservation, restoration or management of biodiversity, ecosystem processes or services, and (b) improve the ability of crops and livestock to maintain crop yields under climate change and/or by buffering biophysical impacts of extreme weather events or increased temperatures. To be appropriate for smallholder farmers, these practices must also help increase their food security, increase or diversify their sources of income generation, take advantage of local or traditional knowledge, be based on local inputs, and have low implementation and labor costs. To illustrate the application of this definition, we provide some examples from smallholders’ coffee management practices in Mesoamerica. We also highlight three key obstacles that currently constrain the use of Ecosystem-based Adaptation practices (i) the need for greater understanding of their effectiveness and the factors that drive their adoption, (ii) the development supportive and integrated agriculture and climate change policies that specifically promote them as part of a broader agricultural adaptation program; and (iii) the establishment and maintaining strong and innovative extension programs for smallholder farmers. Our framework is an important starting point for identifying which Ecosystem-based Adaptation practices are appropriate for smallholder farmers and merit attention in international and national adaptation efforts.