Guided inquiry learning is an effective method for learning about scientific concepts. The present study investigated the effects of combining video modeling (VM) examples and metacognitive prompts on university students' (N = 127) scientific reasoning and self-regulation during inquiry learning. We compared the effects of watching VM examples combined with prompts (VMP) to watching VM examples only, and to unguided inquiry (control) in a training and a transfer task. Dependent variables were scientific reasoning ability, hypothesis and argumentation quality, and scientific reasoning and self-regulation processes. Participants in the VMP and VM conditions had higher hypothesis and argumentation quality in the training task and higher hypothesis quality in the transfer task compared to the control group. There was no added benefit of the prompts. Screen captures and think aloud protocols during the two tasks served to obtain insights into students' scientific reasoning and self-regulation processes. Epistemic network analysis (ENA) and process mining were used to model the co-occurrence and sequences of these processes. The ENA identified stronger co-occurrences between scientific reasoning and self-regulation processes in the two VM conditions compared to the control condition. Process mining revealed that in the VM conditions these processes occurred in unique sequences and that self-regulation processes had many self-loops. Our findings show that video modeling examples are a promising instructional method for supporting inquiry learning on both the process and the learning outcomes level.