Agroecology integrates ecological principles into the management of agricultural systems. Therefore, the aims of this study were: (i) to characterize livelihoods in terms of capital theory, (ii) to determine agroecological performance on farms led by rural Montubio farmers. In the tropical region of the Ecuadorian Chocó, 38 surveys were conducted with Montubio heads of households. The questionnaire had two sections: (1) livelihoods and (2) agroecological elements, and several statistical tests were carried out. Farms headed by women are 2.55 ha larger in area, and the area for crops and pastureland in farms led by men is 2.11 ha smaller. Challenges persist in access to land deeds and external income. The women excelled in resilience (7.14%), diversity (6.86%), and social values (4.97%), while their male counterparts did better in responsible governance (8.80%). The study showed gender differences in the livelihoods and agroecological performance of farms led by Montubios.