The agricultural intensification of farming systems in sub-Saharan Africa is a prerequisite to alleviate rural poverty and to improve livelihood. In this modelling exercise, we identified sustainable intensification scenarios for maize-based cropping systems in Ethiopia. We evaluated Conventional Intensification (CI) as continuous maize monocropping using higher Mineral Fertilizer (MF) rates with and without the incorporation of Crop Residues (CR) in the soil. We also evaluated the effect of groundnut in rotation with the maize-based cropping system with the current Farmer’s Practice + Rotation (FP + Rotation) and increased MF application rates (CI + Rotation) combined with CR incorporation. The results suggest that, under CI, there was a positive effect of MF and CR. The incorporation of only CR in the field increased the maize yield by 45.3% compared to the farmer’s yield under current MF rates. CR combined with higher MF (60 kg N ha−1 + 20 kg P ha−1) increased the yield by 134.6%. Incorporating CR and MF was also beneficial under rotation with groundnut. The maize yields increased up to 110.1% depending upon the scenarios tested. In the scenario where CR was not incorporated in the field, the maize yield declined by 21.9%. The Gross Economic Profit suggests that groundnut in rotation with maize is advantageous across Ethiopia in terms of the net return with a few exceptions.