Enhancing nutrient use efficiencies (NUEs) is an important factor in achieving the long-term sustainability of a production system. Our two-year experiment was aimed at accessing the NUEs of the integration of macro- and micronutrient fertilization responses of three lentil (Lens culinaris) cultivars. Three cultivars were planted in the main plots, and ten nutrient combinations were used in the sub-plots: N1, control; N2, 100% recommended dose of fertilizers (RDF) (20:40—N:P2O5); N3, vermicompost (VC) at 2 t ha−1; N4, 50% recommended dose of nitrogen (RDN) + 100% recommended dose of phosphorus (RDP) + VC at 1 t ha−1; N5, RDF + 0.5% ZnSO4; N6, RDF + 0.5% FeSO4; N7, RDF + 0.5% ZnSO4 + 0.5% FeSO4; N8, 50% RDN + 100% RDP + VC at 1 t ha−1 + 0.5% ZnSO4; N9, 50% RDN + 100% RDP + VC at 1 t ha−1 + 0.5% FeSO4; and N10, 50% RDN + 100% RDP + VC at 1 t ha−1 + 0.5% ZnSO4 + 0.5% FeSO4. The results show that the cultivar HM-1 (1.59–1.61 Mg ha−1) recorded a significantly higher seed yield than cultivars Sapna (1.31–1.33 Mg ha−1) and Garima (both 1.30 Mg ha−1), while the cultivar Sapna had significantly more stover yield (1.86–1.90 Mg ha−1) than cultivar HM-1 (1.68–1.73 Mg ha−1). Cultivar HM-1 was more efficient in terms of partial factor productivity for N (77.5–78.5 kg kg−1), P (48.2–48.7 kg kg−1), K (143.6–145.5 kg kg−1), Zn (1336–1352 kg kg−1), and Fe (417–421 kg kg−1) than Sapna and Garima. Application of 50% N + 100% P + VC at 1.0 t ha−1 + 0.5% ZnSO4 + 0.5% FeSO4 resulted in higher seed yield (1.63–1.65 Mg ha−1) and agronomic efficiency for N (26.3–28.8 kg kg−1), P (12.42–13.63 kg kg−1), and K (52.3–57.4 kg kg−1) over other tested practices in both years. Hence, it could be concluded that considering the integrated nutrient management paradigm including 10 kg N ha−1 coupled with 40 kg P2O5 ha−1 through synthetic fertilizers, vermicomposting 1.0 t ha−1 as an organic source and foliar spray of 0.5% each of ZnSO4 and FeSO4 (N10) produced a 56.8% higher seed yield than the control, in addition to improving nutrient dynamics and NUEs for N, P, K, Zn, and Fe. Therefore, integrated fertilization coupled with cultivar selection could help to achieve the long-term food and nutritional sustainability targeted by the Sustainable Development Goals (SDGs).