Abstract CONTEXT Integrated crop-livestock systems are facing the pressure to intensify worldwide, yet decoupling crops and livestock can lead to specialized systems relying on greater external inputs and potential negative externalities. OBJECTIVE Our goal was to compare rice-pasture, as the business-as-usual rotation, with two intensified systems, rice-soybean and rice-cover crop, to address the following objectives:1) quantify partial carbon footprint (CF) including both crop and livestock, 2) develop a multi-criteria performance index based on productivity, economic, and environmental indicators at the systems-level, and 3) evaluate the stability of this index over the study period. METHODS To understand how increasing the frequency of annual grain crops influences whole-system sustainability, we evaluated 10 productivity, economic and environmental indicators as well as a multi-criteria performance index and its stability in three rice-based rotation systems over 7 years in Uruguay. Treatments were:(a) rice?pasture [a 5 yr rotation of rice?ryegrass (Lolium multiflorum Lam.)?rice, then 3.5 yr of a perennial mixture of tall fescue (Festuca arundinacea Schreb.), white clover (Trifolium repens L.), and birdsfoot trefoil (Lotus corniculatus L.)], (b) rice?soybean [a 2-yr rotation of rice?ryegrass?soybean (Glycine max [L.] Merr.)? Egyptian clover (Trifolium alexandrinum L.)], and (c) rice?cover crop (an annual rotation of rice?Egyptian clover). RESULTS AND CONCLUSIONS Rice-soybean had medium productivity and energy use, resulting in the highest nitrogen and energy use efficiency and among the lowest yield-scaled C footprint. Field greenhouse gas emissions and embodied energy in fuel and agrochemicals were similar in rice-pasture and rice-soybean, but the increase in soil organic carbon in pasture rotating with rice was able to offset this by almost 50%. Rice-cover crop had the highest economic incomes but also the highest input costs, translating into the lowest gross margin. Although the rice-soybean and rice-pasture had a similar gross margin, the variability in rice-pasture was lower and with lower input costs. Rice-soybean and rice-pasture had a multi-criteria performance index 65% higher than rice-cover crop (0.35). Rice-pasture had the highest overall stability across four different stability parameters calculated. We conclude that the intensification of rice-pasture with annual crops could reduce the stability of sustainability without increasing economic performance, even for rice-soybean that showed the best the multi-criteria performance but with less stability across indicators. SIGNIFICANCE The findings of this study demonstrate how the integration of rice and pastures with livestock achieves the best combination of stability across profitability and environmental performance, thus mitigating vulnerability to external stressors.