In severely deficit soil, lentil (Lens culinaris Medic) crop requires micronutrients for increased production. Micronutrient management is, therefore, very important for lentil productivity but mostly ignored. This study was carried out from 2014–2015 to 2016–2017 to understand the effects of zinc (Zn), boron (B), and molybdenum (Mo) on lentil productivity, nodulation, and nutrient uptake and how these elements improve soil micronutrient fertility. The experiment was laid out in randomized complete block design, and the treatments were replicated thrice. Different combinations of Zn, Mo, and B were contrasted with no application of micronutrients. The treatments were Zn alone (Zn), B alone (B), Mo alone (Mo), Zn combined with B (ZnB), Zn with Mo (ZnMo), B with Mo (BMo), and Zn combined with B and Mo (ZnBMo). Doses of Zn, B, and Mo were 3, 2, and 1 kg ha⁻¹, respectively. In this trial, the highest average seed yield (1807 kg ha⁻¹) and yield increment (44%) was obtained in ZnBMo combined application with macronutrients. Single, dual, and combined application of Zn, B, and Mo had significant effects on yield parameters and yield of lentil (P < 0.05). The highest nutrient uptake, maximum nodulation (63.5 plant⁻¹), and the highest protein content (26.6%) in seed were recorded from the treatment receiving all three micronutrients. The increased lentil yield might be associated with increased nodulation and nutrient uptake by the crop under micronutrient-applied treatments. The results suggest that combination of Zn, B, and Mo could be applied for increased lentil production in micronutrient deficit soils.