Today, more and more universities in Turkey and in the world are teaching all courses in English and many others are preparing to do so by offering a certain percent of content-area courses in English. This tendency reinforces the importance of university EFL preparatory classes where students are taught English, and prepared for further academic studies. However, the right methodology to be used in such language classrooms is still in question among ELT researchers and practitioners.The purpose of this case study was to investigate foreign language instructors’ perceptions of content-based instruction (CBI), and diverse CBI models in Karadeniz Technical University, where content-based instruction was once used but then terminated in the Department of Basic English and is still in use by only some instructors in the Department of Modern Languages. Another aim was to find out the potential advantages and disadvantages of using content-based instruction in university preparatory programs. The findings of the study revealed the controversy in the EFL instructors’ perceptions and practice of content-based instruction, as well as the reasons behind the termination of this methodology.