Mixed farming systems are still prevalent in sub-Saharan Africa. In these systems, the recycling of nutrients through crop-livestock integration (CLI) practices is crucial for the sustainability of soil fertility and crop production. The objective of this study was to analyze nutrient (N, P, K) flows and balances of mixed farming systems to assess CLI contribution to the performance of those systems. We hypothesized that more intensive farms had a better nutrient balance at the farm level, and that improved biomass management methods improved their nutrient balance. Nine farms in the Madagascar highlands were selected, some corresponding to poor traditional farms with only draft cattle; some small or medium-sized, more intensive farms with a dairy herd; and some of the latter with some improvement to management methods of livestock effluents (manure composting, liquid manure collection). The nutrient balance of the farming systems was determined, and performance indicators were calculated at both farming, livestock, and CLI levels. Results showed that nutrient recycling through CLI is significant in the functioning of the systems studied, contributing primarily to circulating nutrient flows (up to 76%) and leading to greater efficiency and productivity. Nutrient flows resulting from these practices mainly concerned animal feeding (higher than 60% of nutrient flows), even if manure management was central for crop fertilization and that manure remained a desired animal product of these types of farms (up to 100% of animal products). Large negative balances of N and K (up to 80% of inputs) were observed in traditional livestock systems with draft cattle. They were smaller (39–68%) in more intensive dairy farms. Composting of manure did not decrease negative balances, whereas their magnitude was significantly reduced by the collection of liquid manure (19% for N; 42% for K). Better management of biomass at the farm level, in particular the collection of liquid manure, seemed to substantially reduce nutrient losses in MFS.