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Abstract Background Rehabilitation is seen as crucial in dealing with the demographic change in many European countries. In Germany, for example, after having stayed in a rehabilitation center, patients have the possibility to participate in aftercare programs aimed at promoting long-term health behaviour. Despite the relevance of follow-up support for patients’ long-term health and work ability, participation rates in aftercare programs are quite low. Here, web-based aftercare programs can be a viable alternative to the traditional face-to-face programs due to their flexibility in time and location. This research project aims to use quantitative and qualitative methods to gain more insight into the potential of web-based aftercare programs. Methods The goal is to recruit up to 1150 patients at baseline in five rehabilitation centers across Germany. For ethical reasons, partially randomized experimental study design is used to quantitatively assess the effectiveness of web-based aftercare programs. All patients are offered the traditional face-to-face aftercare treatment (IRENA). When patients deny to participate in traditional face-to-face aftercare, they are randomly distributed into either web-based aftercare (digIRENA) or a control group. In all three groups, the SF-12, which measures subjective health, and the WAI, which measures working ability, will be used at baseline, 13 weeks, 26 weeks and 43 weeks after the patients have left the rehabilitation center. BREQ-2, which measures motivation, is used only in the traditional aftercare group and the web-based aftercare group. A multivariate analysis of variance with repeated measurement and latent growth curve models will be used to compare the development of the variables in the three groups. For the qualitative part of the study, interviews with patients and therapists will be conducted to shed light on the applicability, acceptance, and usability of web-based aftercare programs. Discussion This study may provide valuable insight into the potential of web-based rehabilitation aftercare programs as a way to supplement traditional face-to-face programs. This seems particularly promising if it can manage to reach those patients who do not currently participate in traditional face-to-face rehabilitation aftercare programs due to time and location constraints. Trial registration The trial has been registered at the German Register of Clinical Studies (DRKS) with the registration number: DRKS00022467 .