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. It provides conceptual and methodological elements for developing and promoting agroecological innovations within country strategies to address agroecosystem resilience in specific production landscapes. This guidance note explains basic agroecological concepts, principles and its application in the design and management of biodiverse and resilient farming systems. Building on the COMDEKS landscape approach, the guide strengthens its agroecosystem component to more effectively build the social, economic and ecological resilience of production landscapes.