The purpose of this study was to identify which question/reflection format leads to the most favorable results in terms of effect on autonomous motivation and appreciation for the intervention in a web-based computer-tailored physical activity (PA) intervention, based on principles from self-determination theory (SDT) and motivational interviewing (MI). For this purpose, a randomized trial was conducted among 465 Dutch adults, comparing three web-based computer-tailored MI/SDT PA interventions, including (i) exclusively open-ended questions (without skillful reflections), (ii) exclusively multiple choice questions (with skillful reflections) and (iii) including both question types (with skillful reflections). Measurements included motivation-related determinants of PA and process variables, measured at baseline, directly following the intervention and 1-month post-intervention. Results suggest that open-ended questions represent an important element in web-based MI in terms of effect on autonomous motivation. In order to optimize appreciation of the intervention, a combination of both open-ended and multiple choice question types seems to hold most promise. The findings of this study suggest that both open-ended and multiple choice questions should be included in web-based computer-tailored SDT/MI PA interventions. More research is needed to reveal the optimal configuration of this novel intervention type.