Internationally in secondary schools, lessons are typically taught by subject specialists, raising the question of how to accommodate teaching which bridges the sciences and humanities. This is the first study to look at how students make sense of the teaching they receive in two subjects (science and religious education [RE]) when one subject's curriculum explicitly refers to cross-disciplinary study and the other does not. Interviews with 61 students in seven schools in England suggested that students perceive a permeable boundary between science and their learning in science lessons and also a permeable boundary between religion and their learning in RE lessons, yet perceive a firm boundary between science lessons and RE lessons. We concluded that it is unreasonable to expect students to transfer instruction about cross-disciplinary perspectives across such impermeable subject boundaries. Finally, we consider the implications of these findings for the successful management of cross-disciplinary education.