In soils, cysteine and methionine represent the predominant constituents of the low molecular weight organic S, but their role in plant nutrition and soil S cycling is unclear. Cysteine and methionine uptake by pot-cultivated wheat and oilseed rape and their cycling were evaluated using 14C and 35S labelling. About 0.16%–0.30% of 14C from cysteine and methionine was absorbed by the plants after 6 h, indicating that the plants could utilise organic S, with oilseed rape showing higher ability than wheat to take up intact organic S and its derivative inorganic S. Plants utilised organic S with much lower efficiency than inorganic S because most organic S was decomposed by microorganisms. Nitrogen (N) addition enhanced plant S uptake, as high N uptake stimulates S immobilization. About 28%–33% and 67–71% of 14C from cysteine and methionine, respectively, were retained in the microbial biomass (MB), a much higher proportion of 14C from cysteine was released as 14CO2 from the soil than from methionine. Further, 16%–25% and 61%–72% of 35S from cysteine and methionine, respectively, were retained in the MB, and 35%–42% and 5%–9% were released from it as SO42−. Microbial carbon (C) and S use efficiency for cysteine was lower than for methionine, whereas plants utilised higher amounts of cysteine-derived S as sulphate. The higher microbial utilisation rate of methionine by soil microorganisms, compared with cysteine, may reduce the bioavailability of this compound in the soil solution, and, consequently, its uptake by plants.