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Plasma levels of branched-chain amino acids (BCAA) and aromatic amino acids (AAA) are considered early metabolic markers of obesity and insulin resistance (IR). This study aimed to assess changes in plasma concentrations of BCAA/AAA and HOMA-IR2 (homeostasis model assessment of IR) after intervention-induced modifications in fat mass (FM) and fat-free mass (FFM) among French Polynesian adolescents. FM, FFM, plasma levels of BCAA and AAA, HOMA-IR2 were recorded at baseline and post intervention among 226 adolescents during a 5-month school-based intervention on diet and physical activity. Participants were divided into two subgroups according to their college attendance status which determined their intervention adherence: externs/half-residents (n = 157) and residents (n = 69). Four ordinal categories of body composition changes post-intervention were created for the analysis (FM^gain/FFM^lost < FM^gain/FFM^gain < FM^lost/FFM^lost < FM^lost/FFM^gain). After 5 months, changes in BCAA (<i>p</i>^−trend < 0.001) and AAA (<i>p</i>^−trend = 0.007) concentrations were positively associated with ordinal categories of body composition. HOMA-IR2 significantly decreased with FM^lost (−0.40; 95% CI, −0.60 to −0.20) and increased with FM^gain (0.23; 95% CI, 0.11 to 0.36). Our results suggest that FM loss is associated with a decrease in concentrations of obesity and IR metabolic markers which is more substantial when FM loss is accompanied with FFM gain.