Agroecology proposes to mobilize the scientific and practical, traditional and local knowledge of producers to develop jointly new production systems. This article presents the results of research on biological control carried out since 2003 in the north of Uruguay. Experiences were conducted by different organizations of family farmers and by BIO-Uruguay (Batoví Instituto Orgánico), a social organization founded by family farmers and rural inhabitants. The results of the analyzed experiences are technical, methodological and social, focusing mainly on the biological fight against pests and diseases of agricultural and livestock production. The different stages of the co-innovation process are presented to obtain biological solutions from the recognition and use of native pathogenic fungi to control pests of economic importance. The objectives of this study were to restore biological balances, to contribute to the agroecological transitions of the productive systems, and to enforce the collective learning, necessary among the actors, for co-innovation. These learnings contribute to the development of the individual and institutional capacities needed to "build agroecology" in Uruguay.