The present study investigated the effects of question prompts in scaffolding novice instructional designers solving ill-structured, instructional design problems in a Web-based learning environment. The effects of question prompts were studied under different prompting conditions (Question-Elaboration vs. Question-Guidance), taking into consideration various levels of learners' prior knowledge and experience. The study employed a comparative, multiple-case study design using the technique of think-aloud protocols, which were followed by interviews. Eight graduate students from the program of Instructional Design and Technology participated in the study. While the qualitative findings supported the previous research on the advantages of question prompts in scaffolding ill-structured problem solving, they also shed light on the specific cognitive and metacognitive functions, as well as limitations, of question prompts in different conditions. The study has implications for designing instructional scaffolds for supporting ill-structured problem solving of various domains in a Web-based learning environment.