Characterizing and understanding the complexity of numerous interactions occurring in mixed farming systems is still a methodological challenge. We hypothesize that farm functioning features in terms of crop-livestock integration practices impact the agroecological performance of the system, which will be also affected by the farm context. In order to analyze crop-livestock integration in a holistic way, a set of seventeen mixed farming systems from three contrasting socioeconomic regions of the humid tropics (Guadeloupe, Brazilian Amazonia, and Cuba) was selected in order to cover a wide range of crop-livestock integration situations. The ecological network analysis was applied to each farm in order to study the nutrient flow networks, expressed in nitrogen. The activity and flow organization of crop-livestock integration practices were characterized and the agroecological performance has been evaluated in terms of efficiency, resilience, productivity, and dependency of N flow networks. Here, we show for the first time that the range of crop-livestock integration is well characterized by the activity and organization of flows. Gradients of crop-livestock integration were well detected and described. Some agroecological performances were related to a particular socioeconomic context. Resource endowment influenced efficiency, according to the intensification level. The crop-livestock integration however contributed partially to the productivity of the system, being especially effective in promoting resilience. This study applies a suitable framework to analyze complex farming systems while linking their functioning and performance in an agroecological approach. Thus, comparison of contrasting systems was feasible here with the support of numerical and tangible figures for interpreting complex indicators (e.g., resilience), representing a useful tool for monitoring sustainability of agricultural systems in a dynamic and holistic way.