We analyze the influence of dietary counseling and physical activity on biochemical and metabolic parameters in children and adolescents with HIV. A longitudinal experimental study, including three analyses: At the beginning, 4th month, and 8th month. A sample of 18 subjects with HIV of both sexes, mean age 10.4 ± 4.50 years. Usual food intake (24 h recall and food intake marker), level of habitual physical activity, biochemical parameters, resting metabolic rate, as well as body composition (dual-energy X-ray absorptiometry), biological maturation, and anamnesis with clinical data and socioeconomic were evaluated. There was an effect of time on the reduction of blood glucose and triglycerides and the resting metabolic rate. There was a significant increase in fruit consumption throughout the study. The consumption of soft drinks decreased when comparing analysis periods 1 and 2, however, it increased again in analysis period 3. There was no significant effect of time on the set of variables related to a food recall. Counseling healthy habits and regular clinical follow-up were relevant for improving biochemical parameters (glucose, triglyceride, HDL cholesterol), maintaining the resting metabolic rate, increasing fruit consumption, and decreasing the consumption of soft drinks, in part of the time, of children and adolescents with HIV. Finally, we emphasize that counseling positively influenced healthy habits, and these, in turn, improved health-related parameters.