Physical inactivity is one of the major risk factors for poor health in the world. Therefore, effective interventions that promote physical activity are needed. Hence, we developed an eHealth intervention for adults, i.e., 'MyPlan 1.0', which includes self-regulation techniques for behaviour change. This study examined the effect of 'MyPlan 1.0' on physical activity (PA) levels in general practice. 615 adults (≥18 years) were recruited in 19 Flemish general practices, for the intervention group ( = 328) or for the wait-list control group ( = 183). Participants in the intervention group received the web-based intervention 'MyPlan 1.0' and were prompted to discuss their personal advice/action plan with their general practitioner. Participants in the wait-list control group only received general advice from the website. Self-reported physical activity was assessed with the International Physical Activity Questionnaire (IPAQ) at baseline and after one month. A three-level (general practice, adults, time) regression analysis was conducted in MLwiN. Significant intervention effects were found for total PA and moderate to vigorous PA with an increase for the intervention group compared to a decrease in the control condition. However, there was a high dropout rate in the intervention group (76%) and the wait-list control group (57%). Our self-regulation intervention was effective in increasing physical activity levels in adults. Future studies should consider strategies to prevent the large dropout from participants.