Studies of the impact of nitrification inhibitors (NIs), specifically DMPP and DMPSA, on N2O emissions during “hot moments” have produced conflicting results regarding their effectiveness after rewetting. This study aimed to clarify the effectiveness of NIs in reducing N2O emissions by assessing residual DMP concentration and its influence on ammonia-oxidizing bacteria (AOB) in two pot experiments using calcareous (Soil C, Calcic Haploxerept) and acidic soils (Soil A, Dystric Xerochrepts). Fertilizer treatments included urea (U), DMPP, and DMPSA. The experiments were divided into Phase I (water application to dry period, 44 days) and Phase II (rewetting from days 101 to 121). In both phases for Soil C, total N2O emissions were reduced by 88% and 90% for DMPP and DMPSA, respectively, compared with U alone. While in Phase I, the efficacy of NIs was linked to the regulation of AOB populations, in Phase II this group was not affected by NIs, suggesting that nitrification may not be the predominant process after rewetting. In Soil A, higher concentrations of DMP from DMPP were maintained compared to Soil C at the end of each phase. Despite this, NIs had no significant effect due to low nitrification rates and limited amoA gene abundance, indicating unfavorable conditions for nitrifiers. The study highlights the need to optimize NIs to reduce N2O emissions and improve nitrogen efficiency, while understanding their interactions with the soil. This knowledge is necessary in order to design fertilization strategies that improve the sustainability of agriculture under climate change.