Sleep disorders are catching attention worldwide as they can induce dyshomeostasis and health issues in all animals, including humans. Circadian rhythms are biological 24-hour cycles that influence physiology and behavior in all living organisms. Sleep is a crucial resting state for survival and is under the control of circadian rhythms. Studies have shown the influence of sleep on various pathological conditions, including metabolic diseases; however, the biological mechanisms involving the circadian clock, sleep, and metabolism regulation are not well understood. In previous work, we standardized a sleep disturbance protocol and, observed that short-time sleep deprivation and sleep-pattern alteration induce homeostatic sleep regulation, locomotor deficits, and increase oxidative stress. Now, we investigated the relationship between these alterations with the circadian clock and energetic metabolism. In this study, we evaluated the expression of the circadian clock and drosophila insulin-like peptides (DILPs) genes and metabolic markers glucose, triglycerides, and glycogen in fruit flies subjected to short-term sleep disruption protocols. The sleep disturbance altered the expression of clock genes and DILPs genes expression, and modulated glucose, triglycerides, and glycogen levels. Moreover, we demonstrated changes in mTor/dFoxo genes, AKT phosphorylation, and dopamine levels in nocturnal light-exposed flies. Thus, our results suggest a connection between clock genes and metabolism disruption as a consequence of sleep disruption, demonstrating the importance of sleep quality in health maintenance.