Background In the past years, robotic systems have become increasingly popular in upper limb rehabilitation. Nevertheless, clinical studies have so far not been able to confirm superior efficacy of robotic therapy over conventional methods. The personalization of robot-aided therapy according to the patients' individual motor deficits has been suggested as a pivotal step to improve the clinical outcome of such approaches. Methods Here, we present a model-based approach to personalize robot-aided rehabilitation therapy within training sessions. The proposed method combines the information from different motor performance measures recorded from the robot to continuously estimate patients' motor improvement for a series of point-to-point reaching movements in different directions. Additionally, it comprises a personalization routine to automatically adapt the rehabilitation training. We engineered our approach using an upper-limb exoskeleton. The implementation was tested with 17 healthy subjects, who underwent a motor-adaptation paradigm, and two subacute stroke patients, exhibiting different degrees of motor impairment, who participated in a pilot test undergoing rehabilitative motor training. Results The results of the exploratory study with healthy subjects showed that the participants divided into fast and slow adapters. The model was able to correctly estimate distinct motor improvement progressions between the two groups of participants while proposing individual training protocols. For the two pilot patients, an analysis of the selected motor performance measures showed that both patients were able to retain the improvements gained during training when reaching movements were reintroduced at a later stage. These results suggest that the automated training adaptation was appropriately timed and specifically tailored to the abilities of each individual. Conclusions The results of our exploratory study demonstrated the feasibility of the proposed model-based approach for the personalization of robot-aided rehabilitation therapy. The pilot test with two subacute stroke patients further supported our approach, while providing encouraging results for the applicability in clinical settings.