In this paper, we report a case study of a 16-year-old Swedish upper secondary student's developing understanding of key concept areas studied in his upper secondary school chemistry course. This study illustrates how the thinking of an individual learner, Jesper, evolves over a school year in response to formal instruction in a particular educational context. Jesper presented a range of ideas, some of which matched intended teaching whilst others were quite inconsistent with canonical chemistry. Of particular interest, research data suggest that his initial alternative conceptions influenced his thinking about subsequent teaching of chemistry subject matter, illustrating how students' alternative conceptions interact with formal instruction. Our findings support the claims of some researchers that alternative conceptions may be stable and tenacious in the context of instruction. Jesper's rich conceptualisation of matter at submicroscopic scales drew upon intuitions about the world that led to teaching being misinterpreted to develop further alternative conceptions. Yet his intuitive thinking also offered clear potential links with canonical scientific concepts that could have been harnessed to channel his developing thinking. These findings support the argument that identifying students' intuitive thinking and how it develops in different instructional contexts can support the development of more effective science pedagogy.