This study investigated the effects of the flipped classroom model on EFL learner autonomy in a content-based instructional context. The participants involved were students enrolled in two linguistics classes, divided into an experimental group (n = 64) which received a flipped classroom (FC) instruction and a control group (n = 60) taught in a non-flipped classroom. In the FC, various functions were embedded in a Moodle course management system (CMS), including video lectures, online quizzes, resources and e-journals. The comparison between the pre- and post-questionnaire on perceived learner autonomy showed no difference between the groups prior to instruction; however, significant statistical differences were found between the groups following instruction, especially in the constructs of learner autonomous strategy, learner behavior and learner confidence. The examination of e-journals revealed that learner autonomy had been improved in terms of strategy use, behavior, interaction with the materials, the use of social resources and self-management of learning. The CMS log analysis showed significant correlations between online learning activities and perceived learner autonomy. Furthermore, the data collected from the pre- and post-questionnaires, e-journal and interviews were analysed and interpreted to explain the fostered learner autonomy from psychological, technical, sociocultural and political-critical perspectives.