Chronic diseases may affect the nutritional status of children and adolescents. Calcium (Ca), phosphorus (P), and vitamin D (Vit-D) are crucial nutrients for their growth and development. Proper diagnosis and treatment are critical components of personalized and precision medicine. Hence, we conducted a cross-sectional and comparative study to evaluate Ca, P, and Vit-D levels in their non-skeletal functions and their association with health and nutritional biomarkers in children and adolescents with diverse chronic conditions. We performed anthropometric, body composition, clinical evaluation, biochemical analysis, and dietary survey methods. A total of 78 patients (1–19 years, 43 females, 42 children) took part in this study. Overall, 24, 30, and 24 participants were obese, undernourished, and eutrophic, respectively. Results found that 74% and 35% of individuals had deficient Vit-D and Ca intake, respectively. Most cases were normocalcemic. Results also found that 47% of the subjects had Vit-D deficiency (VDD), 37% were insufficient, and 37% had hypophosphatemia. Of the 46% and 31% of patients with VDD and insufficient levels, 19% and 11% were hypophosphatemic, respectively. Calcium, P, and Vit-D levels were associated with anthropometric parameters, body mass index, body composition, physical activity, diet, growth hormones, and the immune, liver, and kidney systems. These results show the coincident risk of altered Ca, P, and Vit-D metabolism in children and adolescents with chronic diseases.