This guide is intended to serve as the basis for the implementation of the Innovative Agro-ecology component of the GEF Small Grants Programme in its 6th Operational phase, and to provide guidance for the agro-ecosystem outcome of the COMDEKS landscape approach. In particular, this guidance aims to enable communities to make meaningful contributions to agroecosystem resilience in selected production landscapes, by providing guidance on tools and methods that can be used to engage smallholder organizations in the participatory analysis of agroecosystem vulnerability to impacts of climate change, and other social and economic factors as well as the identification of resilience outcomes, as well as to help communities to identify agroecosystem vulnerability and resilience enhancing innovations, how to test and implement these innovations, monitor progress and analyze and evaluate results.