During long distance migration, many birds may experience periods of either prolonged fasting, during endurance flights, or extensive feeding during stopovers. It was previously shown that habitat selection during stopover can largely affect the migration outcome of an individual. Despite decades of research of the avian metabolism during stopover and migration, many questions have remained unanswered, as such research mainly focused on targeted metabolites and fat metabolism. Here, we examined the plasma-metabolome of migrating passerines prior to their crossing the Sahara Desert. Birds were sampled at two sites populated by Pistacia trees, bearing fat-rich fruits, and at an additional site dominated by blooming Eucalyptus trees. The blood samples were analyzed using both GC-MS and LC-MS, using an untargeted approach. We found that birds from one of the sites had a distinguish metabolic profile, suggesting recent landing. Examination of metabolic pathways activated during stopovers indicated a crucial role for cycling glucose through the Cori and Cahill cycles in resting and recovery processes. This novel perspective, conducted on free-ranging birds, suggests the evolution of avian insulin resistance due to factors such as endurance exercise, fasting, and a preference for fatty acid oxidation during migration, akin to cell trauma recovery. Additionally, we investigated inter-site variations in birds' metabolic profiles. Significant variations were observed in both polar and lipophilic metabolites among the sites. Differences in polar metabolites were primarily attributed to variations in the physiological state of the birds between sites, while distinctions in the lipophilic profiles of rested birds were linked to variations in their primary food sources. This study underscores the challenge of interpreting commonly used indicators for assessing migrating birds' physiological states and site quality, which are predominantly derived from lipid metabolism, in complex ecological systems.