Learning in medical education encompasses a broad spectrum of learning theories, and an embodiment perspective has recently begun to emerge in continuing professional development (CPD) for health professionals. However, empirical research into the experience of embodiment in learning in CPD is sparse, particularly in the practice of general medicine. In this study, we aimed to explore general practitioners’ (GPs’) learning experiences during CPD from an embodiment perspective, studying the appearance of elements of embodiment—the body, actions, emotions, cognition, and interactions with the surroundings and others—to build an explanatory structure of embodiment in learning. We drew on the concepts of embodied affectivity and mutual incorporation to frame our understanding of embodiment. Four Danish and three Canadian GPs were interviewed to gain insight into specific learning experiences; the interviews and the analysis were inspired by micro-phenomenology, augmented with a complex adaptive systems approach. We constructed an explanatory structure of learning with two entrance points (disharmony and mundanity), an eight-component learning phase, and an ending phase with two exit points (harmony and continuing imbalance). All components of the learning phase—community, pride, validation, rehearsal, do-ability, mind-space, ambiance, and preparing for the future—shared features of embodied affectivity and mutual incorporation and interacted in multi-directional and non-linear ways. We discuss integrating the embodiment perspective into existing learning theories and argue that CPD for GPs would benefit from doing so.