Direct belowground nitrogen (N) transfer has often been reported where plants with contrasting nutrients acquisition strategies (N2-fixing and non-fixing) co-occur, and there is still a gap in the knowledge of the extent of this transfer in the top soil under the field conditions. However, assessment under field conditions is challenging. We hypothesized a practical application of the analysis of natural abundance of δ15N supplemented with an isotopic mixing model ‘IsoSource’ to understand the relative direct contribution of N2-fixing Alnus acuminata to wheat intercrop (non-fixing) N isotopic signatures. A field experiment was conducted in an andic soil of high lands in northern Rwanda to quantitatively determine the proportional contribution of nitrogen by Alnus acuminata to wheat vegetative tissue isotope signatures at different distances from the trees (1 m, 3 m, 5 m, and 7 m). The study involved the measurements and analyses of natural abundance of stable isotopes δ15N and isotopic mixing modeling by IsoSource. Leaf samples were collected from twigs of 10 years old Alnus acuminata grown on the terrace-risers, along with soil samples (0–20 cm) and wheat flag leaf samples across terrace at 1 m, 3 m, 5 m, and 7 m from trees for isotopic measurement. The chlorophyll content index of wheat flag leaf at the four points across terrace was estimated by means of SPAD meter 502. The δ15N proportional contribution by Alnus acuminata to wheat was obtained through IsoSource analysis. We noted a significant (p < 0·01) gradient in depletion of wheat δ15N signatures moving further away from the tree line of Alnus acuminata. The wheat at 1 m from the trees exhibited the δ15N values closer to that of the tree, while at 7 m, the crop δ15N signature was significantly different from that of the tree. An isotopic mixing model ‘IsoSource’ indicated that the tree N may have provided 33·6 ± 4·3 % of the wheat intercrop N at 1 m distance from the trees. Therefore, this study shows that the understanding of field-based crop N and nutrient transfer in agroforestry may be enhanced by analysis of the physiological basis of stable isotopes signatures.