Many primary teachers face challenges in teaching inquiry science, often because they believe that they do not have the content knowledge or pedagogical skills to do so. This is a concern given the emphasis attached to teaching science through inquiry where students do not simply learn about science but also do science. This study reports on the reflections of nine grade 6 teachers who taught two cooperative, inquiry science units once a term for two consecutive school terms. The study focused on investigating their perceptions of teaching inquiry science as well as the processes they employed, including the benefits and challenges of this student-centred approach to teaching, with longer task structures that characterises inquiry learning. Although the teachers reflected positively on their experiences teaching the inquiry science units, they also expressed concerns about the challenges that arise when teaching through inquiry. Implications for teacher education are discussed.