We sought to identify metabolites that mark the relationship of sugar-sweetened beverage (SSB) intake with adiposity and metabolic risk among boys (n = 114) and girls (n = 128) aged 8–14 years. We conducted the analysis in three steps: (1) linear regression to examine associations of SSB intake (quartiles) with adiposity, glycemia, lipids, and blood pressure (BP); (2) least absolute shrinkage and selection operator (LASSO) regression to identify SSB-associated metabolites from an untargeted dataset of 938 metabolites; and (3) linear regression to determine whether SSB-related metabolites are also associated with adiposity and metabolic risk. In girls, SSB intake was associated with marginally higher BP (Q2 vs, Q1: 1.11 [−3.90, 6.13], Q3 vs. Q1: 1.16 [−3.81, 6.13], Q4 vs. Q1: 4.65 [−0.22, 9.53] mmHg systolic blood pressure (SBP); P-trend = 0.07). In boys, SSB intake corresponded with higher C-peptide insulin resistance (Q2 vs. Q1: 0.06 [−0.06, 0.19], Q3 vs. Q1: 0.01 [−0.12, 0.14], Q4 vs. Q1: 0.17 [0.04, 0.30] ng/mL; P-trend = 0.03) and leptin (P-trend = 0.02). LASSO identified 6 annotated metabolites in girls (5-methyl-tetrohydrofolate, phenylephrine, urate, nonanoate, deoxyuridine, sn-glycero-3-phosphocholine) and 3 annotated metabolites in boys (2-piperidinone, octanoylcarnitine, catechol) associated with SSB intake. Among girls, urate and nonanoate marked the relationship of SSB intake with BP. None of the SSB-associated metabolites were related to health outcomes in boys.