The role of circadian clocks in regulating metabolic processes is well known; however, their impact on metabolic states across species and life stages remains largely unexplored. This study investigates the relationship between circadian rhythms and metabolic regulation in the Drosophila larval fat body, a metabolic hub analogous to the mammalian liver and adipose tissue. Surprisingly, the fat body of period null mutants, which lack a functional circadian clock in all tissues, exhibited 12-h rhythms in gene expression, particularly those involved in peroxisome function, lipid metabolism, and oxidative stress response. These transcriptomic rhythms were aligned with 12-h oscillations in peroxisome biogenesis and activity, reactive oxygen species levels, and lipid peroxidation. Furthermore, period mutants exhibited 12-h rhythms in body fat storage, ultimately leading to a net reduction in body fat levels. Collectively, our results identify clock-independent ultradian rhythms in lipid metabolism that are essential for larval survival and development.