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Migratory birds undertake long journeys across continents to reach breeding habitats with abundant resources. These migrations are essential for their survival and are shaped by a complex interplay of physiological adaptations, behavioral cues, and gene expression patterns. Central to migration are stopovers, critical resting points where birds replenish energy stores before continuing their journey. In this study, we integrate physiological measurements, behavioral observations, and molecular data from temporarily caged migrating Garden Warblers (Sylvia borin) to gain insights into their stopover strategies and physiological adaptations after crossing the extended ecological barrier formed by the Sahara Desert and the Mediterranean Sea. Depleted individuals, marked by low body mass and flight muscle mass, showcased remarkable plasticity in recovering and rapidly rebuilding energy stores within a short 5‐day stopover. Flight muscle mass increased during this period, highlighting a dynamic trade‐off between muscle rebuilding and refuelling. Notably, birds prioritizing muscle rebuilding exhibited a trade‐off with the downregulation of genes related to lipid transport and metabolism and at the same time showing evidence of skeletal muscle angiogenesis. Early arrivals were more motivated to depart and exhibited higher levels of physiological stress. Our study highlights the importance of understanding the adaptive responses of birds to changing environmental conditions along their migration routes. Research highlights: Rapid energy store replenishment in depleted Garden Warblers during stopoversDynamic trade‐off between muscle rebuilding and refuellingEarly arrivals exhibit higher motivation and stress response, influencing migration decision‐making [ABSTRACT FROM AUTHOR]