This study checked the nitrogen (N) uptake, fate of the N fertilizer, fertilizer recovery efficiency (FRE) and the residual amount of N fertilizer in the soil via 15 N-labelled fertilizer applied to soybean (Glycine max L. Merr.), to explain any differences in the yields. Two soybean field experiments were established in Brazil, one conducted in a tropical (Trop) zone located at Cerrado Biome and the other in a subtropical (Subt) environment. The experimental design was a 2-factor in randomized complete block with four replications. Five doses of N (0, 20, 40, 80 and 120 kg ha −1) were applied at two soybean growth stages (VE and R3). For all treatments, except No-N, 15 N-labelled fertilizer was used. The N uptake and the amount of N fertilizer were analysed in the roots, shoots, grains and whole plant, the FRE and yield by soybean, and the residual of fertilizer in the soil. The total N uptake (Nplant) was greater with fertilization at R3 stage compared to the other stage, and N application increased the yield just at this stage and in the Trop condition. The increase in N shoot (not specifically from fertilizer) with the application at R3 appeared to be related to the increased in yield. However, the N from fertilizer found in the plant shoot was about 20% higher when fertilizer was applied at VE compared with R3. Under Subt condition, the FRE averaging 55%. In contrast, the FRE decreased from low to high nitrogen rates (64 to 40%, respectively) when soybean grown under Trop condition. Most N from fertilizer (38%) was found in the grains, followed by the shoot (14.6%) and the root (0.58%). The use of N fertilizer at reproductive growth stages is a better approach to meet soybean N demand through N fertilization. Potential yield gains are more reliable under Trop condition.