Soybean is Brazil´s most important grain crop and accumulates over 250 kg N ha−1, principally from biological N2 fixation. The residual N benefit depends heavily on the quantity of the belowground N at harvest, much of which cannot be directly recovered in roots. The purpose of this study was to investigate different aspects of the 15N shoot-labelling technique to quantify non-recoverable N in rhizodeposits. Three pot experiments were performed and the aerial tissue was labelled with highly enriched 15N-labelled urea or glutamine at between 27 and 39 days after planting. In all experiments sequential harvests were taken until late grain-filling phase. After only 2 or 3 days between 5.8 and 21.3% of enriched N was found in the soil but the excess 15N deposited until the final harvest was in all cases less than twice this amount, respectively. Evidence obtained suggested that this early deposition of labelled N was an artefact of the labelling technique. Discounting this initial tracer N decreased estimates of rhizodeposited N by between 51 and 66%. Nodules were much lower in 15N enrichment than roots. Nodule N constituted 39 to 76% of belowground N, such that the inclusion of none or all of this N to calculate the 15N enrichment of the roots increased the estimates of rhizodeposited N by between 34 and 58%. We conclude that even if the immediate post-labelling deposition of enriched N is discounted, estimates of rhizodeposited N of nodulated legumes will not be reliable.