The study of avian migration physiology has advanced substantially in the past few decades, yet despite the key role of migratory stopovers in influencing total migration time, our knowledge on the physiological control of this crucial stage is still scarce. Research in stopover physiology has recently taken new directions and uncovered new mechanisms which help us understand how multiple internal factors, such as body condition or fuelling rate, interact with one another to trigger the rapid metabolic and behavioural switches that underlie stopover decisions. In this paper, we review a series of studies that our group conducted during the last 14 years on the island of Ponza (Italy), an important stopover site for thousands of small passerines migrating from Africa to Europe in spring. Focusing on nocturnally migrating passerines, we first discuss the pivotal role of fuel stores in decision-making processes during stopover. We then present recent research on the effects of food availability and fuel accumulation on behaviour shown by migrants at stopover places. Finally, we summarise recent findings on the hormonal factors that participate in controlling the switch between non-migratory and migratory state. Although the review is focused on our studies, we include recent work by other groups in this field.