In no-tillage rotation systems, the recovery of nitrogen (N) fertilizer in the soil–plant system is affected by soil fertility and biological changes caused by the surface application of lime (L) and phosphogypsum (PG). Here we assessed the effect of surface-applied L and/or PG on the fate of 15N-labeled fertilizer, soil chemical properties, microbial gene copy number (16 S rRNA of prokaryotes and genes of N cycle) and grain yield of maize (Zea mays L. intercropped with ruzigrass) in rotation with soybean [Glycine max (L.) Merrill] during two growing seasons. We found that applying L improved soil fertility, particularly when combined with PG (LPG treatment), resulting in higher grain yield. Moreover, compared with the control, the recovery of 15N-labeled ammonium sulfate [(15NH4)2SO4] increased in maize and ruzigrass dry matter but decreased in soybean grown on the residue of the first growing season in two treatments (L and LPG). The losses of 15N-labeled fertilizer were highest in the control and PG treatments. A large amount of 15N-labeled fertilizer was found in the deep layers of PG-amended soil, indicating leaching of fertilizer-derived 15N. Conversely, the analysis of soil microbial N cycle genes revealed that the abundances of denitrifiers were highest in the control (no correctives applied), suggesting that the N fertilizer remaining in the soil increased denitrification rates. Surface application of a combination of L and PG is clearly a feasible strategy for increasing soil fertility, 15N recovery from fertilizer, and grain yield while reducing environmental pollution associated with nitrification and denitrification.