Sustainability measurement addresses the social, economic, and environmental aspects in order to support policy and decision-making. In the Peruvian Amazon, some smallholder livestock farmers have subsisted through time, partially preserving the ecosystems and demonstrating in practice a certain degree of sustainability. In this regard, this study aims at measuring the sustainability of smallholder livestock farming in the Peruvian Amazon. Sustainability was measured using a multi-criteria method, through the construction of sustainability indicators based on information obtained from field surveys, and soil and macrofauna sampling in the pastures. For this purpose, economic, environmental, and socio-cultural indicators were considered, with a rating scale from 0 to 4, where 0 is the least sustainable category and 4 is the most sustainable one. Smallholder livestock farming was considered sustainable if the general sustainability index (GenSI) was equal to or greater than 2 and, at the same time, if none of the three indicators had a value lower than 2. The socio-cultural indicator was within the sustainability threshold, but the economic and environmental indicators did not fulfill the necessary requirements to consider smallholder livestock farming a sustainable activity in the city of Yurimaguas, Peru. The critical points affecting the sustainability of smallholder livestock farming in Yurimaguas were as follows: degraded soils, lack of silvopastoral systems, inefficient transport system, low annual income, and low levels of associativity. The results suggest the need for mitigating these limitations, as well as promoting associativity and implementing silvopastoral systems for the improvement of the welfare of smallholder livestock farmers.