While substantial nitrogen (N) input from yak urine in intensively grazed grasslands on the Qinghai-Tibetan Plateau (QTP) is well documented, the species-specific responses of dominant forage plants—particularly regarding N uptake efficiency, environmental impacts, and associated microbial dynamics—remain poorly understood. This study investigated Elymus nutans (Gramineae) and Kobresia graminifolia (Cyperaceae), two ecologically dominant species, to elucidate the divergent nitrogen transformation features under urine deposition. During the growing season, we simulated yak urine input by applying 640 mL urine per 40 cm × 40 cm patch in natural grasslands. Over six weeks, we measured total plant N uptake and soil nitrous oxide (N₂O) emissions and evaluated soil nitrification rates through a 2-week indoor incubation experiment. To elucidate the underlying microbial mechanisms, we analysed the abundance and composition of rhizosphere ammonia-oxidizing archaea (AOA) and bacteria (AOB). Results showed that K. graminifolia exhibited significantly lower soil nitrification rates and N₂O emissions but higher total N uptake compared to E. nutans. Furthermore, K. graminifolia soil had lower AOB and higher AOA abundances. Specifically, the relative abundances of Nitrosophaera and Candidatus Nitrosocosmicus within AOA, as well as Nitrosovibrio and Nitrosomonas within AOB, were higher in K. graminifolia soil. These findings indicate that variations in nitrifier populations may be key drivers of differences in N uptake and N₂O emissions across dominant forage species. This study provides valuable insights for developing effective management strategies for intensively grazed grasslands on the QTP.