To increase Europe’s self-sufficiency for protein sources, boosting plant protein production is a prerequisite. Yield variability is one of the main problems regarding the cultivation of protein crops. In this light, cereal–legume intercropping can offer a solution, as well-balanced intercropping systems are less prone to yield variations. Therefore, in this study the effects of (i) species/genotype combination, (ii) intercropping sowing densities and (iii) fertilizer regime were evaluated under Belgian (Northwestern European) conditions over three years (i.e., the 2020–2021, 2021–2022 and 2022–2023 seasons). Regarding the species combinations, winter barley x winter pea, winter wheat x winter faba bean and winter triticale x winter faba bean, it was observed that the best-performing combination varied from year to year depending on the prevailing weather conditions. A reduced sowing density (i.e., 130 seeds/m2 for the cereal partner and 20 seeds/m2 in the case of faba bean or 40 seeds/m2 in the case of pea) was sufficient to achieve competitive yields under the prevailing conditions. Inoculation with commercial Rhizobium strains did not result in an increased yield. Fertilization with one or two nitrogen fractions significantly increased the total yield thanks to a yield increase in the cereal partner; however, as a consequence, the proportion of legumes in the mixture decreased. In conclusion, it can be stated that with the investigated cereal–legume combinations, a competitive yield and qualitative protein yield can be achieved with a reduced fertilizer input.