The aim of the study was to assess the impact of sulphur and molybdenum fertilization on the yield and chemical composition of common bean seeds. A field experiment was conducted in southeastern Poland in 2012–2014. The scheme of the study included the following treatments: O-control, Mo-molybdenum (100 g·ha−1), SBS-sulphur before sowing (50 kg·ha−1), SFA-sulphur foliar application (50 kg·ha−1), Mo + SBS-molybdenum (100 g·ha−1) and sulphur before sowing (50 kg·ha−1), and Mo + SFA-molybdenum (100 g·ha−1) and sulphur foliar application (50 kg·ha−1). After harvesting, the following determinations were made in bean seeds: content of nitrogen, sulphur, phosphorus, potassium, calcium, magnesium, methionine, and cysteine. Application of Mo increased seed yield and protein and methionine content, as well as the content and uptake of P, Mg, and Ca in common bean seeds. Sulphur application had a positive effect on seed yield (13.6% increase) and protein content. Moreover, sulphur improved the biological value of protein by increasing the content of methionine, cysteine, and some macroelements. The most beneficial effects were obtained when both molybdenum and sulphur were used in fertilization. Considering the yield-producing effect and the impact on the biological quality of protein, sulphur fertilization should be included in the crop management for the common bean.