The family milpa system (FMS) is of great importance to food security and the livelihoods of rural families in Mexico. However, the performance of the system can be compromised due to inappropriate agricultural practices. Therefore, a suitable evaluation strategy is required to identify the best management of resources. Nonetheless, at present, there is no holistic understanding around the nature–society interface that allows us to predict the global behavior of the FMS. Thus, this study assesses the global performance of a Poblano FMS through emergy-based indices. The emergy evaluation was carried out by accounting for the available energy of different qualities used in the system, which were subsequently converted to one kind of energy (solar emjoules). The percentage of renewable emergy (%Ren) used in the system was 72.16%. The emergy self-support ratio (ESR) showed that 74% of the emergy used came from free local resources. The emergy investment ratio (EIR) of 0.36 indicated that the emergy use was efficient. The emergy yield ratio (EYR) was 3.78, which in terms of net emergy (NE), was equivalent to a gain of 1.35 × 10¹⁶ sej ha⁻¹ y⁻¹. The environmental loading ratio (ELR) was 0.39, which indicated a low potential environmental impact. The emergy sustainability index (ESI) was high (9.80) compared to other agricultural systems. The performance of the FMS is superior compared to other agricultural systems, including ecologic and recycling systems. However, the use of resources is not optimum and needs to be improved to reach maximum empower.