Research-intensive teacher education programmes aim to educate teachers to work in an inquiry-based manner, meaning that they should be able to use and conduct research to reflect on their teaching. Little is known, however, about how graduates of these programmes function and develop as teachers. In this study seven graduates of Dutch academic teacher education programmes were followed to investigate how their inquiry-based working developed during their first years of teaching. Interviews were conducted with these graduates and their school leaders over three subsequent years. Their involvement in inquiry-based working was found to shift from the classroom level to the school organisational level, with this shift being dependent on individual and organisational conditions. The results suggest ways to support teachers' professional development in inquiry-based working.