The deficiency of micronutrients and low organic matter (OM) status of soils are major hurdles in the optimum crop yield achievements. Humic substances can play an imperative role in the micronutrient bioavailability and improved crop yield by ameliorating the physicochemical soil properties. consumed as fresh food and in processed form. However, its susceptibility towards micronutrient deficiency causes a significant reduction in yield. That is why a current study was done to examine the influence of different potassium humate (KH) levels, i.e., 0, 5, 10, and 15 kg ha−1 with micronutrients mixture (MC), i.e., 0, 50 (Zn = 2.50, B = 0.75, Fe = 2.50 kg ha−1), 75 (Zn = 3.75, B = 1.125, Fe = 3.75 kg ha−1) and 100% (Zn = 5.0, B = 1.5, Fe = 5.0 kg ha−1) on the yield, biomass, harvesting index and uptake of the micronutrients in tomato. The results showed that increasing the level of K-humate significantly improved the yield (7.4 and 7.17%), total biomass (6.38 and 6.59%), and harvesting the index (0.46 and 0.76%) of tomato. It also enhanced Fe uptake but did not affect B and Zn concentrations in the tomato fruit at 100% MC + 15 kg ha−1 KH over control in the autumn and spring seasons. In conclusion, both levels of K-humate 10 and 15 kg ha−1 and MC 75 and 100% effectively enhance the yield, biomass, harvesting the index, and micronutrients (B, Zn, and Fe) uptake in tomatoes.