The traditional local genotype, EPACE-10, has a higher grain protein content (GPC) but a lower yield than the commercial genotypes, Gurguéia or Novaera. This study aimed to evaluate whether the GPC and quality or productivity of these different genotypes could be affected by top dressing fertilization with nitrogen (N) or phosphorus (P). In the first experiment, EPACE 10 and Gurguéia were subjected to the following treatments: inoculated with Rhizobium and only inoculated with N fertilization 25 days after sowing (DAS) or at the first flowering stage. In the second experiment, EPACE-10 and Novaera were subjected to the following treatments: inoculated only; inoculated plus mono ammonium phosphate (MAP) or urea applied at the pollination stage. In both experiments, none of the treatments resulted in an increase in GPC for each genotype. However, treatment with N at 25 DAS in the first experiment and with MAP in the second experiment increased methionine and cysteine content in EPACE 10, while treatment with N in the second experiment increased methionine content in Novaera. Therefore, in both trials, the top dressing fertilizer treatments increased the yield of EPACE 10 to the same level as Gurguéia or Novaera. Furthermore, the local genotype EPACE 10 exhibited a positive response to P fertilization, resulting in increased methionine and cysteine content and yield specific to its genotype.