We examined the development of task-specific couplings among functional subsystems (i.e., ball circulation, respiration, and body sway) when learning to juggle a three-ball cascade, with a focus on learning-induced changes in the coupling between ball movements and respiration and the coupling between ball movements and body sway. Six novices practiced to juggle three balls in cascade fashion for one hour per day for twenty days. On specific days (7 in total), ball movements, center-of-pressure (CoP) trajectories and respiration traces were measured simultaneously. Discrete, time-continuous and spectral analyses revealed that the spatio-temporal variability of the juggling patterns decreased with practice and that the degree to which the task constraints were satisfied increased gradually. No conclusive evidence was found for ball movement-respiration coupling. In contrast, clear-cut evidence was found for the presence of 1:3 and 2:3 frequency locking between the vertical component of the ball trajectories and both the anterior-posterior and the medio-lateral components of the CoP. Incidence and expression of these mode locks varied across individuals and altered in the course of learning. Gradual changes in locking strength, appearances and disappearances of mode locks, as well as abrupt transitions between coupled states were observed. These results indicate that dissimilar learning dynamics may arise in the functional embedding of subsystems into a task-specific organization and that motor equivalence is an inherent property of such emerging task-specific organizations.