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The application of transition theories to the study of alternative food networks (AFNs) have improved the understanding of innovation processes triggered by the networks of actors during agro-ecological transitions. However, these models often reduce the categories of scale and territory as repositories of variables that define the dual relationship between the agro-ecological niche and the corporate food regime. In an attempt to overcome the static and dualistic niche-regime relation and, to capture the multidimensionality of innovation processes implicit in the agro-ecological transition pathway, we present an analytical model based on the precepts of: territorial configurations, social construction of agro-ecological markets, reflexive governance and scale as a social strategy. We applied this model to the analysis of agro-ecological transitions in two municipalities in the Paraíba Valley and in the Northern Coast of São Paulo, Brazil. We show that technological innovations and the generation of new knowledge in the transition process are dependant on the social skills of the actors involved in building broad social coalitions and reflexive governance spaces capable of converting knowledge into practices that result in the inclusion of family farmers in the scaling-up of agro-ecological transitions. [ABSTRACT FROM AUTHOR]