Cropping systems in the lowlands of temperate South America have been based on irrigated rice and beef-cattle production. Plough-and-harrow is still the most used method to prepare the soil after a season of irrigated rice, but it causes high soil disturbance and is time- and energy-demanding. To improve the sustainability of a rice–soybean rotation system, we studied an alternative method for soil preparation based on a heavy knife-roller. This method was evaluated during three cropping seasons and compared to the plough-and-harrow, applied after the harvest of irrigated rice in a flat hydromorphic soil in south Brazil. In the subsequent summer, soybean was seeded using a no-tillage seeder. Observations on soybean establishment and grain yield demonstrated that the alternative method performed as well as the plough-based system. Benefits of the roller-based method were a 50% reduction in energy consumption for soil preparation, corresponding to a 22% increase in overall energy use-efficiency of soybean production. Labour time and greenhouse gas emissions for soil preparation were reduced with 29 and 55%, respectively. Next to these savings, the roller-based method can also be performed shortly after rice harvest, creating better opportunities for cover crops or pastures in between rice and soybean. In conclusion, the equivalent agronomic and superior sustainability performance makes the knife-roller method an appealing alternative for seedbed preparation after irrigated rice in lowland production systems.