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Adequate supply of micronutrients is important for the proper growth and yield of lentil, particularly in poorly fertile soil. This study was carried out to understand the effects of zinc (Zn), boron (B), and molybdenum (Mo) on the growth and yield of lentil, and how these elements can help manage soil fertility issues. In this regard, the morpho-physiological traits of lentils (BARI Masur-7) were collected from two experiments receiving the same treatments carried out during consecutive rabi seasons of 2015–2016 and 2016–2017. The experiments were laid out with a randomized complete block design having eight treatments, and was replicated thrice. The treatments were T1 (Control), T2 (Zn2.0 kg ha−1), T3 (B1.5 kg ha−1), T4 (Mo1.0 kg ha−1), T5 (Zn2.0B1.5 kg ha−1), T6 (Zn2.0Mo1.0 kg ha−1), T7 (B1.5Mo1.0 kg ha−1), and T8 (Zn2.0B1.5Mo1.0 kg ha−1). The results revealed that the application of micronutrients either singly or in combination had significant effects on the plant height, number of branches per plant, number of pods per plant, number of seeds per pod, thousand seed weight, and the seed yield of lentil. The maximum seed production was, however, observed in plots receiving treatment T8, i.e., the combined application of Zn, B, and Mo. Agronomic biofortification also had significantly increased protein content of lentil seeds while affecting the macro and micronutrient content of lentil seed. These results suggest that any micronutrient deficiencies might lead to a yield loss of lentil, and such a scenario could be avoided by a combined application of micronutrients at a proportionate level.