This contribution belongs to a larger empirical study that focuses on issues related to the implementation of inquiry-based learning and formative assessment in science and mathematics education, while it also refers to the issue of STEM education. Here, we discuss the two topics from the perspective of professional preparation of primary school teachers. We employ an educational tool called Concept Cartoons and perceive it as a common diagnostic tool for investigating modes of reasoning about general statements in arithmetic, geometry and biology. The presented qualitative exploratory empirical study maps and codes various kinds of reasoning that can be identified with the tool and investigates possibilities of a joint coding procedure. As a result, it provides a conversion table between various modes of reasoning in the three subject domains. The arisen code categories cover the field of generic examples, including the initial stages so that they can be used for scaffolding the process of learning the foundations of deductive reasoning. The joint approach to reasoning in mathematics and biology shows how argumentation and formative assessment can be understood equally and developed simultaneously in both school subjects. It helps us to see how the two school subjects can be integrated didactically.