The goal of the AG-Innovation agent-based model is to explore and compare the effects of two alternative mechanisms of innovation development and diffusion (exogenous, linear and endogenous, non-linear) on emergent properties of food and income distribution and adoption rates of different innovations. The model also assesses the range of conditions under which these two alternative mechanisms would be effective in improving food security and income inequality outcomes. Our modelling questions were: i) How do cross-scalar social-ecological interactions within agricultural innovation systems affect system outcomes of food security and income inequality? ii) Do foreign aid-driven exogenous innovation perpetuate income inequality and food insecurity and if so, under which conditions? iii) Do community-driven endogenous innovations improve food security and income inequality and if so, under which conditions? The Ag-Innovation model is intended to serve as a thinking tool for for the development and testing of hypotheses, generating an understanding of the behavior of agricultural innovation systems, and identifying conditions under which alternated innovation mechanisms would improve food security and income inequality outcomes.