Today’s life has demonstrated that online education, which is believed to be more efficient when autonomous, will dominate the education process. This study investigates whether there are any significant constraints concerning learner autonomy implementation in secondary school virtual classrooms in Hatay, Turkey. The data were collected using both quantitative and qualitative data collection tools. For the quantitative data, a questionnaire was administered to 194 teachers working at state and private secondary schools to explore learner autonomy perceptions and language teaching practices promoting learner autonomy. To support the quantitative data, semi-structured interviews were conducted with 21 EFL teachers volunteering to participate. Findings revealed that the EFL teachers are having difficulty promoting learner autonomy due to the fact that they are assumed to be practising traditional approaches which cannot be appropriate in online EFL teaching and learning environment. Moreover, learner autonomy promotion is challenging in an online learning setting for several reasons, such as time, curriculum, and class-size limitations in addition to teacher-related and learner-related constraints. The findings of this study may contribute to the ELT field in terms of identifying challenges in learner autonomy encouragement in virtual language classrooms.