Background/Objectives: The main objective of this study was to examine the association between lifestyle patterns (physical activity, screen and sleep time and diet) and abdominal obesity, and endocrine, metabolic, and immunological biomarkers in adolescents with Down syndrome (DS). Methods: Eighty-three DS adolescents (38.6% girls), aged 11 to 18 years, from the UP&DOWN study were included. Cluster analysis was performed by including the compliance of recommendations of lifestyle variables, such as moderate to vigorous physical activity (MVPA), screen and sleep time and adherence to the Mediterranean diet (AMD). The waist-to-height ratio was used as an indicator of abdominal obesity. Haematological, biochemical and inflammatory biomarkers were analysed. Results: A three-cluster solution was identified: Cluster 1: adolescents with low compliance; Cluster 2: youth with medium compliance; and Cluster 3: adolescents with high compliance. Significant differences in MVPA (p = 0.000), screen time (p = 0.004), sleep time (p = 0.0001), AMD (p = 0.000) and abdominal obesity (p = 0.003) were found. Clusters 2 and 3 had lower levels of triglycerides and LDL-cholesterol than Cluster 1. Cluster 2, in which all adolescents met the MVPA recommendations, had the lowest levels of galactin 3. Conclusions: Compliance with lifestyle recommendations (PA, screen and sleep time and AMD) and the absence of abdominal obesity seem to be associated with better biochemical and inflammatory values.