Integrated science teaching is a task which requires that teachers develop new conceptual structures for the science topics they teach. It is often assumed that changes in teaching can be facilitated through reflective practices such as teacher self-assessment. Does self-assessment in fact help teachers develop new conceptual structures in the context of integrated science? We examine this assumption in the research reported in this paper. In the German PING project—an integrated science project for middle schools—teacher in-service education was based on collaborative workshops in which a group of 22 teachers from different types of schools used teaching materials for eight integrated topics for their lesson planning and conducting units over a period of 30 months. During this time concept maps, interviews and questionnaires were used as means to promote teacher self-assessment. We find that this kind of self-assessment in a collaborative framework was a useful basis for helping science teachers develop integrated conceptual structures and we suggest that in-service courses might use self-assessment for reflection on conceptual content knowledge as a basis for supporting integrated science teaching.