Dynamic representations (e.g., dynamic geometry software GeoGebra for mathematics learning and PhET simulations for science learning) offer excellent opportunities for students to conduct investigations and to formulate explanations for the visualized phenomena. In order for this to be effective, students need guidance, for example, for planning their investigations and reflecting on their actions. One way to support students is by prompting them by using questions that are adapted to the students’ current situation. This chapter focuses on how pre-service teachers provide guidance for students through questioning and by both structuring and problematizing student learning. Data comes from science lessons taught by pre-service primary school teachers and mathematics lessons taught by pre-service subject teachers. The analysis focused on the different question types the pre-service teachers used as well as how their questioning was adapted to students’ situation. The results show how the pre-service teachers used questions both to structure student thinking and to problematize their answers and reasoning. Questioning was not always adapted to the students’ needs. We propose that adapting teacher questioning to student thinking requires balancing between structuring and problematizing and high level of interpretation from the teacher. Teachers’ skills for interpretation are still beyond the skills of software. Implications for teaching with dynamic representations are discussed.