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Organic amendments (OM) can profoundly affect soil nitrous oxide (N2O) emissions via changing nitrogen (N) cycles. However, mechanistic insights into how nitrification inhibitors modulate the responses of soil N2O emissions to successive application of OM are currently lacking. In this study, we performed a laboratory-scale experiment to examine N2O emissions from tropical vegetable soils subjected to six years of chemical fertilization (CF) or chemical fertilization combined with manure application (CFM), and further evaluated the mitigation effectiveness of the nitrification inhibitor dicyandiamide (DCD) under each management regime. Isotopocule mapping (δ15NSPN2Oand δ18ON2O/H2Omap) showed bacterial nitrification/fungal denitrification contributed 77.4%–88.5% of total N2O production among treatments during the emission peak. The cumulative N2O emissions from the CFM-treated soils were nearly 8-fold of those from the CF-treated soils. CFM stimulated N2O production from bacterial nitrification and denitrification by increasing the abundance of genes linked to nitrifers (AOB and comammox) and denitrifiers (nirK/Sand qnorB), respectively. Moreover, DCD decreased cumulative N2O emissions by averagely 73.3%, with better mitigation performance observed in the CFM treatment due to stronger inhibited nitrification and increased abundance of nosZ, and altered bacterial community composition. The 16S sequencing further revealed that adding DCD to CFM-treated soils resulted in declines in abundance of bacterial phylum Actinobacteriaand Chloroflexithat positively affected N2O emissions; while the opposite pattern prevailed for Gemmatimonadetesthat negatively affected N2O emissions.This study highlights manure application coupled with nitrification inhibitors can achieve the dual goals of enhancing soil fertility while reducing environment risk in tropical agricultural soils.