BACKGROUND: Type 2 diabetes (T2D) in adolescents is associated with an unfavorable lipid profile, but lipoprotein particle subspecies and branched-chain amino acid (BCAA) data are scarce. OBJECTIVE: To evaluate lipoprotein particle distributions, lipoprotein insulin resistance index (LP-IR), and BCAA levels longitudinally and their relationships with sex, race/ethnicity, treatment, and loss of glycemic control in adolescents with youth-onset T2D. METHODS: Participants from the TODAY study (n = 348) had samples analyzed yearly for glycated hemoglobin and nuclear magnetic resonance lipoprotein and BCAA assessments. RESULTS: At baseline, participants with were 13.7 years old with T2D, obesity, and from racial and ethnic minority groups (32.2% Non-Hispanic Black [NHB], 43.7% Hispanic). Smaller low-density lipoprotein (LDL) and larger very low-density lipoprotein (VLDL) sizes, higher high-density lipoprotein (HDL) particle number, and increased LP-IR score predicted worsening of glycemic control. LDL, HDL, and VLDL particle numbers increased over 3 years with weaker trends for decreasing LDL and HDL size. LP-IR and BCAA levels were higher longitudinally in those who lost glycemic control. Females had larger HDL size than males at baseline and throughout. NHBs had the largest LDL and HDL sizes, smaller VLDL size, and lower LP-IR and BCAA. CONCLUSION: These data in youth with T2D demonstrate a progressive atherogenic lipoprotein phenotype over 3 years. Increased LP-IR and BCAA are associated with worsening glycemic control and may be contributing to the premature development of atherosclerosis in youth with T2D.