This study aimed to determine the associations of targeted metabolomics and hormone profiles data with lean mass index (LMI), which were estimated using bioelectrical impedance, in survivors of child severe malnutrition (SM) (n = 69) and controls (n = 77) in Malawi 7 years after being treated. Linear associations between individual metabolite or hormone and LMI were determined, including their interaction with nutrition status 7 years prior. Path analysis was performed to determine structural associations. Lastly, predictive models for LMI were developed using the metabolome and hormone profile by elastic net regularized regression (EN). Metabolites including several lipids, amino acids, and hormones were individually associated (p < 0.05 after false discovery rate correction) with LMI. However, plasma FGF21 (Control: β = -0.02, p = 0.59; Case: β = -0.14, p < 0.001) and tryptophan (Control: β = 0.15, p = 0.26; Case: β = 0.70, p < 0.001) were associated with LMI among cases but not among controls (both interaction p-values < 0.01). Moreover, path analysis revealed that tryptophan mediates the association between child SM and LMI. EN revealed that most predictors of LMI differed between groups, further indicating altered metabolic mechanisms driving lean mass accretion among SM survivors later in life.