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This article examines the process of agroecological research on beekeeping systems, developed jointly by the Temperate Agriculture Program of the Brazilian Agricultural Research Company (EMBRAPA), and the Institute of Sociology and Peasant Studies (ISEC), of the University of Córdoba. The investigation was carried out on different beekeeping experiences in southern Brazil: peasant family farms, settlements of agrarian reform, and Afro-descent quilombola and Guarani indigenous villages. The systems are managed in the contexts of agroecological farming and include “Africanized honeybees” and native “stingless bees,” integrated among trees and crops. We show that the dynamics of investigation that follows the guidelines presented by family farmers and traditional people contribute to their empowerment and to changing their own reality, favoring endogenous development and the dialogue of knowledge. The participatory experiences by ISEC and EMBRAPA Temperate Agriculture through the organization and mobilization of farmers and traditional people generated organizational structures that build local food systems. This joint initiative contributes to peasants’ search for autonomy and food sovereignty, and strengthens the reproduction of this work toward the political dimension of agroecology.