To maximise carbon (C) storage in soils, understanding the fate of C originating from aboveground and belowground residues and their interaction with fertiliser under field conditions is critically important. The use of ¹³C natural abundance provides unique opportunities to separate both C sources. We investigated the effect of 16 years of C3 straw and C4 root input, with and without nitrogen (N) addition, on SOC stocks and C distribution in soil fractions in the long-term frame trial at Ultuna, Sweden. The straw C input was fixed at 1.77 Mg ha⁻¹ year⁻¹, while the root input depended on maize plant growth, enabling studies on how N fertilisation affected (i) stabilisation of residues and (ii) plant C allocation to belowground organs. Four treatments were investigated: only maize roots (Control), maize roots with N (Control + N), maize roots and straw (Straw) and maize roots, straw and N (Straw + N). After 16 years, 5.6–8.9% of the total SOC stock in the 0–20 cm soil layer was maize-derived. In all four treatments, the relatively labile SOC fractions decreased, while the proportion of more refractory fractions increased. Based on allometric calculation of root inputs, retention of maize roots was 38, 26, 36 and 18% in the Control, Control + N, Straw and Straw + N treatments, respectively. The estimated retention coefficient of C3 straw in the Straw + N treatment was higher than that in the Straw-N treatment. We interpreted these results thus (1) roots were better stabilised in the soil than straw; (2) N fertilisation caused a shift in root to shoot ratio, with relatively more roots being present in N-deficient soil; and (3) N fertilisation caused greater stabilisation of residues, presumably due to increased microbial C use efficiency.