The study explores the effect of varying levels of nitrogen (N) application on N allocation in Indian mustard (Brassica juncea) genotypes from vegetative to the generative phases. The use of a heat map and PCA biplot analysis identifies two distinct sets of ideotypes. The first set is represented by genotype IC212031 having “Stay-green” phenotype with effective N regulating enzymes, high N uptake (NUpt) and better root development. The second set of ideotype is represented by HB9902 having delayed flowering phenology phases. The study highlights the relevance of Nitrate reductase (NR) in the final oil buildup in seeds (r = 0.5, p = 0.09). The considerable rise in NR activity from pre-anthesis to post-anthesis stages translates to higher seed storage compounds such as oil (r=−0.65, p = 0.03). And the developed prediction models confirmed the significance of these stages (pre-anthesis and post-anthesis) in the accumulation of seed storage components with emphasis on oil content. Similarly, this prediction model helps us to study the cause and effect relationship between various factors and oil content. The notable rise in Nitrite reductase (NiR) activity during the post-anthesis phase suggests its role in assimilating N for the storage of seed components, most likely proteins. Further, the inverse relationship between seed N (−0.53,p= 0.09) and oil content (−0.65, p= 0.03) confirmed that at the post anthesis stage the allocation of N towards precursor carbon compounds happens, which in turn forms either proteins or lipids. This becomes a critical factor in determining the final composition of the seed. Irrespective of N treatment and genotype, the N allocation follows the pattern: seed > siliquae husk > stover > root. However, higher N application rates primarily result in increased NUpt, but not necessarily improve utilisation. Overall, the study highlights the roles of root characteristics, N metabolising enzymes, and flowering phenology in enhancing N allocation and seed production in Indian mustard offering valuable insights for breeding strategies to enhance seed yield, oil content and nutrient efficiency in oilseed crops.