The present study aimed to investigate the influence of genotypic differences on responses to zinc and iron agronomic biofortification among yields of finger millet. A field experiment was conducted over two seasons in farmers’ fields in Ethiopia (2019, 2020). The experimental design had 15 treatment combinations comprising three finger millet genotypes and the applications of different combinations of zinc and iron mineral fertilizers. Five soil-applied fertilizer treatments (20 kg h−1 FeSO4 + 25 kg h−1 ZnSO4 + NPKS, 25 kg ha−1 ZnSO4 + NPKS, 20 kg ha−1 FeSO4 + NPKS, NPKS, and 30% NPKS) at two locations (Gojjam and Arsi Negelle, Ethiopia) and using two slope positions (foot and hill) were replicated four times in a randomized complete block design. Grain yield and biomass were evaluated on a plot basis. Plant height, total and productive tiller number, finger length of the longest spike and number of fingers per main ear were measured at the maturity stage. The combined soil application of FeSO47H2O and ZnSO47H2O increased the yield of the Meba genotype by 51.6%. Additionally, ZnSO47H2O fertilizer application increased the yield of the Urji genotype by 27.6%. A yield enhancement of about 18.3% of the Diga-01 genotype was achieved due to the FeSO47H2O fertilizers’ application. The findings of the present study suggest that the influence of Zn and Fe agronomic biofortification on the yield of finger millet could be affected by genotype differences and environmental conditions.