Learning can be controlled by reflective, ‘cognitive’ or reflexive, ‘habitual’ systems. An essential question is what factors determine which system governs behavior. Here we review recent evidence from navigation, classification, and instrumental learning, demonstrating that stressful events induce a shift from cognitive to habitual control of learning. We propose that this shift, mediated by noradrenaline and glucocorticoids acting through mineralocorticoid receptors, is orchestrated by the amygdala. Although generally adaptive for coping with acute stress, the bias toward habits comes at the cost of reduced flexibility of learning and may ultimately contribute to stress-related psychopathologies.