Significance Shift workers are affected by circadian misalignment and have an increased risk to develop metabolic diseases such as type 2 diabetes. Here, we show that during simulated short-term night shift work insulin sensitivity at the level of skeletal muscle is decreased in male volunteers, which could contribute to the development of type 2 diabetes in the long term. We also find that the muscle molecular clock does not align rapidly to the new behavioral cycle. Importantly, on the level of the transcriptome, circadian misalignment induced upregulation of fatty acid metabolism pathways, potentially resulting in substrate competition on the cellular level. These findings help to better understand the negative consequences during night shift work.