The high grain yield of modern varieties (MV) respond to the increase in fossil-based inputs, and the widespread belief that they are more productive than old varieties (OV) is biased. This belief focuses only on marketable biomass, without considering the consequences on agroecosystem sustainability of the reductions in other portions of NPP. Additionally, field comparisons of OV and MV were normally conducted under industrialized farming conditions, which is detrimental for OV performance. Both trials carried out in this study comparing wheat OV and MV show that, under Mediterranean rainfed conditions and traditional organic management, aerial and belowground biomass production of OV is higher than that of MV, without significantly decreasing yield and enabling a better competition against weeds. From the data of our trials, bibliographic review and information from historical sources, we have reconstructed the NPP and destinations of biomass of Spanish wheat fields (1900–2000). Varietal replacement entailed the reduction in residues and unharvested biomass (UhB), which involved soil degradation in rainfed cereal fields and undermining heterotrophic trophic webs. Our results suggest that OV can increase the sustainability of rainfed Mediterranean agroecosystems at present through the improvement of soil quality, the reduction of herbicides use, and the recovery of biodiversity.