Bats are the only mammals capable of powered flight, allowing them to cover relatively long distances in a short time. However, the general inability of mammals to fuel endurance exercise solely by oxidizing fatty acids may prevent bats from undertaking long-distance intercontinental migrations-like birds do. Here, we conducted untargeted metabolomics to reveal the oxidative fuels used by wild caught Nathusius' pipistrelles. We investigated polar metabolites and lipids in whole blood from bats flying under controlled wind tunnel or field conditions and how metabolites respond to the physiological challenge. Around 70% of detected acyl carnitines were significantly elevated after flight in the wind tunnel compared to resting bats. The phospholipid levels varied; some increased while others decreased significantly after flight, and most did not return to resting levels within 1 h of recovery. During migration season, we observed a significant increase of phosphatidylethanolamines with unsaturated fatty acids and a bulk increase of several phosphatidylcholines and their lyso-derivatives. While migration had a clear effect on phospholipids, recovering after flight in both seasons was less pronounced and only 24% of acyl carnitines were increased after 1 h of rest. We conclude that endurance exercise such as migration has a greater influence on lipid composition and their abundance than short flights, which indicates a relatively high relevance of fatty acid oxidation to fuel migration in bats.