Industrial livestock systems faces a major crisis of legitimacy and animal breeding contributes to this situation. Worldwide, breeding goals focus on economic performance and rarely consider the environmental and social impacts. Agroecology offers a conceptual framework to think alternative solutions to face this crisis and to guide the transition of livestock farming towards nature-based systems. Animal genetics, as an essential component of animal husbandry, should contribute to this evolution. Based on the agroecological principles applied to animal farming and the efficiency-substitution-redesign (ESR) framework, we showed that animal breeding mainly focused on the E-S levels of the ESR framework and few on the redesign of animal farming. We then present some perspectives for the redesign of breeding goals, the use of the G×E interaction information in the evaluation of animals, and the benefits of managing the available genetic diversity of livestock species to fit to the needs of nature-inclusive systems.