A 15 N tracing study was conducted with soils from a long-term nitrogen (N) fertilization experiment to quantify the concurrent gross N transformation rates in soil and the underlying mechanisms for crop yield and N2O emission variability. The treatments were chemical fertilization (NPK, NP, PK, NK), organic fertilization (OF), half chemical/organic fertilization (HOF), and no fertilization (control, CK). The results showed that 30 years of repeated organic or chemical N applications significantly stimulated gross rates of N mineralization and autotrophic nitrification compared with CK. In addition, gross rates of N mineralization (except NP) and autotrophic nitrification (except CK, PK) in all treatments were significantly higher in 2019 (30 years) than in 2007 (18 years). However, the immobilization of mineral N decreased significantly (near to zero) after 30 years of repeated N applications compared to CK or the results of 18 years. The highest maize yields were observed in NPK, but they were not significantly different from HOF yields. The OM yields significantly increased with the duration of the experiment and reached values comparable to NPK yields after more than 12 years of repeated N applications. There was a logarithmic positive relationship between maize yields and gross N mineralization rates (p < 0.01), indicating that it was the key factor explaining the variations in yields. Long-term organic or chemical N applications significantly stimulated N2O emission rates, in line with the stimulation of gross autotrophic nitrification rates. Highest N2O emissions were associated with the organic fertilization treatments. Considering the most suitable climate-smart agricultural practice, taking into account yield, N2O emissions, and carbon sequestration, the combination of organic and chemical N fertilizers can be recommended for the region where the study was carried out.