The report specifically analyses the NIS in Peru and Colombia in the coffee and dairy sectors due to their economic importance for both countries and the large percentage of small producers in these sectors. In order to analyse the NIS, we have utilised an innovations systems approach to form the analytical framework. This framework focuses on four main areas – understanding the actors in the NIS, their roles and attitudes, the patterns of interaction of these actors, and the enabling environment with a focus on small producer inclusion. The research findings confirm that Colombia has a stronger and more operationalized NIS compared to Peru. The main state agencies that have served as a base for the current NIS are COLCIENCIAS (in Colombia) and CONCYTEC (in Peru). Both were founded as Science and Technology Agencies in 1968 and incorporated ‘innovation’ into their functions in 2004 and 2009, respectively. However, even though their historical foundations are similar, they demonstrate large disparities in their growth trajectories, approach and corresponding impacts.