Replacing traditional crop varieties with commercial, high-yielding varieties during the last decades is one of the main drivers for the decline in farmland and crop diversity. However, it is unclear how commercial, high-yielding varieties adapt to less environmental conditions such as weed pressure and mixed cropping cultivation systems. In Europe, organic breeding organizations conserve local, traditional varieties and develop new varieties under low-input conditions, aiming at increasing the range of varieties adapted to harsh cultivation conditions and mixed cropping. To evaluate whether organic varieties (i) cope better with weed pressure and (ii) have a higher adaptability to mixed cropping, we compared the agronomic and quality performance of eight organic varieties with eight commercial, high-yielding varieties, focusing on tomato, the economically most important vegetable in the EU. Each group was cultivated as single plants and in a mixed cropping system, respectively, with a legume and with or without exposure to weed stress by a grass. The organic group outperformed the commercial, high-yielding group, specifically, in mixed cropping systems. Weed stress lowered the yield of both groups, but the organic group showed higher fruit weight stability across the varieties than the commercial, high-yielding varieties when grown as single plants under weed stress.