Understanding the nature of science (NOS) is one of the challenging objectives in science education due, in part, to the complex relationship between religion and science. This study examines how NOS teaching affects the perception of the NOS amongst religious, as compared to secular, students. The participants included 205 religious and secular pre-service teachers; both categories, religious and secular, included Jewish and Muslim students. All students participated in a scientific content course, which integrated activities explicitly addressing the NOS. They completed a closed questionnaire that examined various aspects of NOS perceptions prior to, and following, the course and 22 also participated in semi-structured interviews. A paired "t"-test was performed and the interviews were recorded, transcribed, and analysed. The findings show that the course influenced some aspects of the NOS perceptions amongst all the participants, but did not change the perceived connection between religion and science among the religious participants. The interviews exposed the relationship between religion and science, and the educational implications of the findings are discussed.