Nitrogen (N) transformation in Vattar (stale seed bed) direct-seeded rice requires an understanding of the key microbial functions that fix, mineralize, and oxidize N; however, how these functions co-vary under field-scale N management across crop stages and seasons remains unclear. We conducted two kharif-season experiments in Vattar (stale seed bed) direct-seeded rice at IARI, New Delhi, testing control (no N), recommended split N (Modified-N), and leaf-color-chart (LCC)-guided N at the vegetative and flowering stages, and quantified gene copies of nifH, ureC, and amoA from ammonia-oxidizing bacteria (AOB) and archaea (AOA) by qPCR. Across both years, functional gene abundance showed strong season × stage × treatment interactions, with higher overall gene copy numbers in the second season. Diazotrophs (nifH) and AOA peaked at flowering under low or demand-synchronized N (LCC), whereas ureolysis (ureC) and AOB were most stimulated by modified-N, especially at flowering, indicating a shift toward nitrification under higher inorganic N. Gene-to-gene associations were largely positive, with the strongest coupling between nifH and AOA, and between AOB and AOA. Principal component analysis (PC1 = 54.6%, PC2 = 34.2%) separated the AOA–nifH axis from the AOB–ureC axis, aligned with seasonal and management-driven clustering. Collectively, these results point to a temporally partitioned N cycle in VDSR soils and suggest that demand-synchronized N (e.g., LCC) supports diazotrophs and archaeal nitrification while tempering ureolysis-nitrification dominance, offering a mechanistic pathway to higher N-use efficiency and reduced environmental losses.