Web-based lifestyle interventions are a new area of health research. This randomized controlled trial evaluated the effectiveness of an interactive web-based health program on physical fitness and health. N = 189 healthy adults participated in a 12-week interactive (intervention) or non-interactive (control) web-based health program. The intervention provided a web-based lifestyle intervention to promote physical activity and fitness through individualized activities as part of a fully automated, multimodal health program. The control intervention included health information. Cardiorespiratory fitness measured as maximum oxygen uptake (VO2max) was the primary outcome, while musculoskeletal fitness, physical activity and dietary behavior, and physiological health outcomes were assessed as secondary outcomes (t0: 0 months, t1: 3 months, t2: 9 months, t3: 15 months). Statistical analysis was performed with robust linear mixed models. There were significant time effects in the primary outcome (VO2max) (t0–t1: p = 0.018) and individual secondary outcomes for the interactive web-based health program, but no significant interaction effects in any of the outcomes between the interactive and non-interactive web-based health program. This study did not demonstrate the effectiveness of an interactive compared with a non-interactive web-based health program in physically inactive adults. Future research should further develop the evidence on web-based lifestyle interventions.