High rates of childhood obesity require integral treatment with lifestyle modifications that achieve weight loss. We evaluated a lifestyle intervention on nutrient adequacy and diet quality in children and adolescents with abdominal obesity. A randomized controlled trial was performed on 107 participants, assigned either to a usual care group or to an intensive care group that followed a moderate hypocaloric Mediterranean diet and received nutritional education. Intake adequacy was evaluated using Dietary Reference Intakes and diet quality through the Diet Quality Index for Adolescents (DQI-A), the Healthy Lifestyle Diet-Index (HLD-I) and the Mediterranean Diet Quality Index (KIDMED). Both groups achieved a significant reduction in BMI standard deviation score (BMI-SDS), glucose and total cholesterol levels. Intake of Calcium, Iodine and vitamin D were higher in the intensive care group, with enhanced compliance with recommendations. Higher dietary scores were associated with lower micronutrient inadequacy. DQI-A and HLD-I were significantly higher in the intensive care group vs. usual care group after the treatment. In conclusion, we observed that an intensive lifestyle intervention was able to reduce BMI-SDS in children with abdominal obesity. Furthermore, participants significantly improved dietary indices getting closer to the nutritional recommendations. Therefore, these diet quality indices could be a valid indicator to evaluate micronutrient adequacy.