Sustainable and resilient cropping intensity is now a global focus to address the food demand and nutrition security of the growing population. For sustainable intensification, maintaining soil fertility is a key concern. The nutrient management for the recently developed four crop-based cropping system in Bangladesh has not yet been studied. Hence, field experiments were conducted on the nutrient management of the four crop-based cropping system [Aus (pre-monsoon rice), Aman (monsoon rice), lentil, and mungbean] in calcareous soil in Bangladesh during the years of 2016/17 and 2017/18 to determine the appropriate fertilizer management package to improve crop productivity and sustain soil fertility. The experiment had six treatments assigned in a randomized complete block design with three replications. The treatments included T1 = control (without synthetic fertilizer), T2 = 50% recommended dose of fertilizer (RDF), T3 = 75% RDF, T4 = 100% RDF, T5 = 125% RDF, and T6 = farmers’ practice (FP). The results revealed that the 125% RDF significantly contributed to higher yields of all four crops. The rice equivalent yield (REY) was the highest for the fertilizer management of 125% RDF, which was 45.5%, 9.4%, and 12.2% higher than the control (T1), 100% RDF (T4), and FP, respectively. Considering the uptake of nutrients (N, P, K, S, Zn, and B) by the crops in the cropping system, the 125% RDF was superior to the other treatments. The nutrient management practices had a positive influence on the apparent nutrient recovery (ANR) efficiency of the cropping system. The fertilizer management of 125% RDF was also economically more profitable due to the increment in the cost–benefit ratio of 26.8%, 4.4%, and 4.9% over the control, 100% RDF, and FP, respectively. The results indicate that the current fertilizer recommendations and FP for aus, aman, lentil, and mungbean are not adequate for the change from the three crop to the four crop-based pattern, and an increased dose of fertilizer is required to increase the yield of each individual crop as well as the total system’s productivity. The fertilizer use efficiency is also higher for 125% RDF than the 100% RDF and FP indicating that to sustain the soil fertility in the four crop-based system, the current RDF and FP are not sufficient. This finding will help intensive cropping areas in preventing nutrient deficiencies that would lead to a reduction in the crop yield.