Ecological intensification is crucial for arable organic farmers, in order to partly close the yield gap to conventional yields. One strategy for this is improved management of cover crops, to increase availability of both nitrogen (N), phosphorus (P) and sulfur (S) for the subsequent main crop. However, the potential of cover crops to take up and release nutrients has primarily been determined for aboveground biomass and mostly for N. There have been fewer studies on belowground biomass, and these have focused on recoverable roots. Thus, unrecoverable residues from rhizodeposits and nodules, have been overlooked. The aim of this incubation study was therefore to assess the release of N, P and S from aboveground residues and from intact soil with belowground residues of different cover crop species at low temperature. Shoots and intact soil with roots from seven different cover crops were incubated for 80 days at a temperature of 5 °C. A comparison of the cover crop species revealed a wide variation in nutrient uptake, chemical composition and release of N, P and S, that also varied between shoot and intact soil with roots. Release of N from shoots showed a marked non-stoichiometric behavior, in contrast to the release of P and S, that correlated well with C:P and C:S ratios. N release (from Vicia villosa) and especially P mobilization (from legumes) in intact soil was much greater than the amounts determined in recoverable roots. This shows that unrecoverable pools such as rhizodeposits and fine roots contributed to nutrient release. Garden sorrel (Rumex acetosa) is a promising cover crop regarding uptake and mobilization of P, but also as a multifunctional cover crop for supplying N, K, S and Mg. Hairy vetch (Vicia villosa) is a promising cover crop for N, oilseed radish (Raphanus sativus) for S, P and K, and white lupin (Lupinus albus) for N, P and Mn supply. Based on our results, we propose the use of mixtures of cover crops with different N, P and S uptake and release having the potential to supply a more complete suite of nutrients to the subsequent crop.