Imbalanced nutrient fertilization adversely affects root growth and alters the nutrient use efficiency of a crop. This study aimed to understand the influence of integrated nutrient management on root characteristics and nitrogen use efficiency in the vegetable-based agroecosystem. The field trial was conducted at the Department of Soil Science and Water Management of Dr. Y S Parmar University of Horticulture and Forestry Nauni, Solan (HP) India in 2019 and 2020. There were nine treatments viz. T1- control, T2-100% farmyard manure (FYM; N equivalent basis), T3-100% N, T4-100% NP, T5-100% NK, T6-100% PK, T7-100% NPK, T8-100% NPK + FYM (recommended practice), and T9-150% NPK + FYM on root densities (mass, volume, and length) and N use efficiency of cauliflower and capsicum. The results observed that different treatments exert significant effects on measured as well as derivative parameters. In detail, the application of 150% NPK + FYM recorded significantly higher root-mass density (0.72 and 1.71 g m−3 × 10−3), root-volume density (4.49 and 2.52 m3 m−3 × 10−3), and root-length density (1.21 and 0.81 cm m−3 × 10−4) in cauliflower and capsicum, respectively, which was statistically at par with treatment T9 (100% NPK + FYM). Similarly, this treatment (150% NPK + FYM) resulted in a maximum positive N (774.6 kg ha−1), P (650.4 kg ha−1), and K (334.9 kg ha−1) balance of soil after the complete harvest of two cropping-sequence cycles. However, maximum agronomic N use efficiency (59.9 and 67.9 kg kg−1) and apparent recovery of N (39.3 and 59.7%) were recorded under 100% FYM (N equivalence) in cauliflower and capsicum, respectively, but this treatment produced the negative N balance (−91.7 kg ha−1) and K (−340.3 kg ha−1) in soil, whereas significant improvement in agronomic use efficiency, apparent recovery of applied N, as well as in soil, and the NPK balance was recorded under 100% NPK + FYM over the other treatment. This study recommended an integrated nutrient module that is the application of 100% NPK + FYM to ensure better root growth and positive nutrient balance in the soil.