This longitudinal study aims to provide greater insight into how students' understanding of matter and chemical reactions develops over time and how their knowledge structures are restructured. Four case-study students in a Norwegian primary school were followed for two years from age 10-11 to age 12-13. Researchers were responsible for implementation of science teaching promoting systematic development of students' understanding of the nature of matter and chemical reactions in many contexts across science disciplines. The four case-study students' expressed understanding was recorded and analyzed throughout the period. Results indicate that students develop fragmented and incomplete understanding, and drawing wrong conclusions may be necessary steps in the learning process. Moreover, students seem to develop a somewhat more integrated and cohesive understanding of the nature of matter and chemical reactions, indicating that the students restructure and reorganize their knowledge structures (i.e. differentiation, coalescence and promoting).