The annual nitrogen (N) budget was measured in a soybean-cultivated upland field during the first year after conversion from a paddy field on gray lowland soil, which is typically found on the Sea of Japan side of northern Japan. Forage rice was cultivated on lysimeter fields for 4 consecutive years with applications of chemical fertilizer, immature compost, or mature compost (the control, immature compost, and mature compost plots, respectively), and then the fields were converted to upland fields for soybean (Glycine max [L.] Merrill cultivar Ryuho) cultivation. Input (seed, bulk N deposition, and symbiotic dinitrogen [N2] fixation) and output (harvested grain, leached N via drainage water, and nitrous oxide emission) N flows were measured, and the field N budget was estimated from the difference between the input and output. The soybean plants in the immature and mature compost plots grew well and had higher yields (498–511 g m−2) compared to the control plot (410 g m−2). Total N accumulation in the soybean plants derived from N2 fixation (g N m−2) in the mature compost plot (27.7) was higher than those in the control (18.1) and immature compost plots (19.9). Percentages of soybean N accumulation derived from N2 fixation ranged from 53% to 74%. N derived from symbiotic N2 fixation accounted for more than 90% of the total N input, whereas harvested grain accounted for approximately 85% of the total N output. N leaching mainly occurred during the fallow period, accounting for 13–15% of the total N output. The annual N budgets were negative (−10.0, −14.2, and −6.4 g N m−2 year−1 for the control, immature compost, and mature compost plots, respectively). The N loss from the immature compost plot was higher than that of the control plot, because the N output in harvested grain was higher, and the N input by N2 fixation was similar between plots. While the N loss from the mature compost plot was lower than that of the control plot because the N output in harvested grain was higher, as was the case in the immature compost plot, the N input by N2 fixation was also higher. Preceding compost application––whether immature or mature compost––to paddy fields increased the subsequent soybean yield during the first year after conversion. This result suggests that N loss and the following decrease in soil N availability in the field could be mitigated by increased N2 fixation resulting from mature compost application with an appropriate application practice.