In intensive crop production systems, sustainable agricultural development strives to find the balance between productivity and environmental impact. To reduce the N fertilizer-associated environmental risks of intensive cropping, sound agronomic and environmentally acceptable management practices are urgently needed. To attain high yields, improve soil health, and ensure economic return and N usage efficiency in conservation-based intensive agriculture, N management must be optimized, which has not yet been studied systematically in the mustard-boro rice-aman rice cropping pattern. During 2016/17, 2017/18, and 2018/19 cropping seasons in Bangladesh, cropping system experiments were conducted to investigate the interactive effects of tillage practices and nitrogen fertilizer rates on soil characteristics, crop productivity, and profitability under conservation agriculture (CA) systems. The trial featured two tillage systems: (i) conventional tillage (CT) and (ii) strip-tillage (ST). It also used three doses of N fertilizer: N1: 75% of the recommended N fertilizer dose (RND); N2: 100% of the RND; and N3: 125% of the RND. Each crop’s experiment was set up in a split-plot design with three replications, with the main plot assigned tillage practices and the sub-plot assigned nitrogen fertilizer rates. For rice, neither the tillage systems nor the interactions between the tillage systems and N levels affected any of the growth parameters, yield, and yield components, but the N levels did. Across the tillage systems, the rice grain and straw yield were similar for the N levels of 100% RND and 125% RND, which were significantly higher than the N level of 75% RND. In mustard, the highest seed yield was recorded from the tillage system ST, with an N level of 125% RND, which was at par with the tillage system ST with 100% RND and CT with 125% RND. The highest system rice equivalent yield (SREY, 14.9 to 15.8 t ha−1) was recorded from the tillage system ST, with an N level of 125% RND, which was at par with the same tillage system with an N level of 100% RND. The soil penetration and bulk density (BD) were higher for the CT than the ST, but soil organic matter (OM), total nitrogen (TN), phosphorus (P), potassium (K), and boron (B) content were higher for the tillage system ST than the CT. Across N levels, the tillage system CT had a 2–4% higher production cost than the ST. Total production cost increased as N levels increased across all tillage systems. The tillage system ST with an N level of 125% RND had the highest system gross return and net profit, which was at par with the same tillage system with 100% RND. This study suggested that farmers should apply slightly higher N for the mustard-boro-aman rice systems for the first couple of years when commencing CA; however, after a few years of consistent CA practice, the N rate may be reduced.