<p>Nitrification and nitrogen (N) immobilization are important pathways in soil N transformations, involving soil N loss and retention, respectively. The ratio of nitrification to N immobilization generally reflects the potential risk of soil N loss. However, little is known about the response of this ratio to anthropogenic carbon (C) and N inputs, but also climate and soil conditions. Here, we aimed to elucidate, for the first time, the impacts of chemical fertilizer and manure application on the ratio of gross nitrification to N immobilization by using ¹⁵N dilution technology, based on ten long-term fertilization trials spanning multiple climatic zones in eastern China. Results showed that manure application differentially increased gross N immobilization rather than nitrification compared to the chemical fertilizer treatment, leading to manure-induced decreases in gross nitrification to N immobilization ratio ranging from 1.2 to 93% across the sites. The decreased gross nitrification to N immobilization ratio in the manure treatment was mainly due to the increased ratio of bacteria to nitrifiers abundance. Manuring was more effective for a decrease in the gross nitrification to N immobilization ratio at sites characterized by high rainfall and low soil pH, as it prevented soil pH decline thereby favoring bacterial abundance and N immobilization. Consequently, manure application resulted in a substantial increase in soil total N accumulation, facilitated by increased microbial N immobilization that promoted microbial biomass. These findings suggest that substituting manure for chemical fertilizer in the areas with high rainfall and acidic soils promisingly reduces soil N loss risk, with positive consequences for soil N retention. This knowledge highlights the potential to reconcile soil N loss and fertility improvement through optimizing regional manure management, which offers valuable insights for the development of a tailored regional fertilization management strategy.</p>