This paper presents a flexible approach to model and support inquiry learning processes in complex domains centered around emerging learning objects. It describes our work on applying educational process modeling techniques to provide an agenda-based tool for metacognitive scaffolding that supports students in regulative activities. A prototype has been developed as a pedagogical agent. Rather than presenting the suggested learning sequence directly, the pedagogical agent helps the students to reflect on and possibly re-plan their learning processes by monitoring and analyzing students’ actions and by using a predefined process model. The pedagogical agent has been tested and the initial test results demonstrate the technical feasibility of this approach.