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Soil zinc deficiency in Sub-Saharan Africa (SSA) is a major contributor to poor crop responses to nitrogen, phosphorus and potassium (N, P and K) fertilizer leading to low economic returns on fertilizer use. Despite being drought-tolerant crops, finger millet (Eleusine coracana) and soybean (Glycine max) yields are consistently lower than 1000 kg ha−1 in western Kenya. On-farm trials were conducted in Bungoma and Siaya Counties of western Kenya during two subsequent cropping seasons (long &amp; short rains of 2019) to evaluate the responses of two varieties of finger millet (U15 and SEC915) and soybean (SB19 and SB134) to N, P and K after addition of Zn. Zinc was applied at 0, 1.5, and 3 kg ha−1 and N, P and K at blanket rates. Results showed that application of Zn fertilizer alongside N, P and K fertilizer significantly (p < 0.05) increased grain yields, grain Zn concentration and grain Zn uptake. The largest Zn agronomic efficiency (AEZn) was realized when Zn was applied at 1.5 kg ha−1 for both crops. Application of Zn was profitable (VCR >1) for growing finger millet and soybean in Bungoma and Siaya during long rains and short rains. We recommend applying Zn along with N, P and K fertilizer in Zn-depleted soils to increase finger millet and soybean yields.