Fox nut (Euryale ferox Salisb.) is fast emerging as a super food, and its field cultivation has just started in recent years. To evaluate the impact of secondary and micronutrients on yield and quality of fox nut, a two-year field experiment was conducted with seven treatments involving use of primary (NPK), secondary (Mg) and micronutrients (Zn, Cu and B). Application of Mg @5.0 kg ha−1, Zn @5.0 kg ha−1, B @1.0 kg ha−1 or Cu (foliar spray with 0.1% CuSO4 solution) along with NPK@100, 60 and 40 kg ha−1 increased the relative yield up to 1.46, 1.50, 1.47 and 1.62, respectively, compared to 1.0 at control (no fertilization), 1.26 with NPK, and 1.81 with combined application of Mg, Zn, B and Cu along with NPK. Yield boosting effect of Mg and micronutrients, particularly Cu was mediated mostly through their positive effect on seed weight and size. Secondary and micronutrients application also helped in improving or at least sustaining the seed protein and other nutrients’ content even at higher levels of crop productivity. To our knowledge, this was the first study on fox nut revealing the utility of secondary and micronutrients in improving its yield and quality in subtropical climate.