Web-based lifestyle interventions have attracted considerable research interest. Available evidence on such interventions suggests health-promoting effects, but further research is needed. Therefore, this study aims to investigate short-, medium-, and long-term health effects of a web-based health program (“TK-HealthCoach”, TK-HC) offered by a national statutory health insurance fund (Techniker Krankenkasse, TK). The study comprises two randomized controlled clinical trials to evaluate the health goals “Increasing Fitness” (Fclin) and “Losing and Maintaining Weight” (Wclin). A total of n = 186 physically inactive (Fclin) and n = 150 overweight or obese (Wclin) adults will be randomly assigned to a 12-week interactive (TK-HC) or non-interactive web-based health program using permuted block randomization with a 1:1 allocation ratio. Primary outcomes include cardiorespiratory fitness (Fclin) and body weight (Wclin). Secondary outcomes comprise musculoskeletal fitness (Fclin), physical activity and dietary behavior, anthropometry, blood pressure, blood levels, and vascular health (Fclin, Wclin). All outcomes will be measured before and after the 12-week intervention and after a 6- and 12-month follow-up. Additionally, usage behavior data on the health programs will be assessed. Linear mixed models (LMMs) will be used for statistical analysis. Findings of this study will expand the available evidence on web-based lifestyle interventions.