Seventy-nine students from three science classes conducted simulation-based scientific experiments. They received one of three kinds of instructional support in order to encourage scientific reasoning during inquiry learning: (1) basic inquiry support, (2) advanced inquiry support including explanation prompts, or (3) advanced inquiry support including explanation prompts and regulation prompts. Knowledge test as well as application test results show that students with regulation prompts significantly outperformed students with explanation prompts (knowledge: d = 0.65; application: d = 0.80) and students with basic inquiry support only (knowledge: d = 0.57; application: d = 0.83). The results are in line with a theoretical focus on inquiry learning according to which students need specific support with respect to the regulation of scientific reasoning when developing explanations during experimentation activities.