This paper presents how the process of flipped teaching with Computer Assisted Language Learning (CALL) works in teaching English as a Foreign Language (EFL) writing in the Indonesian context. As well, it also elaborates how the teaching model affects learner autonomy. This flipped teaching with CALL was experienced by some lecturers of private universities in East Java, Indonesia. This study used a multi-site case study research design. The data were yielded from in-class observation, lesson plan analysis, focus group interviews, and questionnaires. The total of 5 EFL writing teachers and 150 students from 5 private universities in East Java, Indonesia had participated in this study. Experimenting with flipped teaching with CALL in teaching EFL writing enabled the teachers, as course developers, to get an idea of their students' response to the challenges of new ways, methods, and techniques of their study. The flip-class environment fostered better communication amongst learners and learner autonomy as well. The flip-class atmosphere also had a beneficial impact on the motivation of learners. The qualitative results from interviews of the learners showed that the learners had inspired themselves to engage in in-class learning activities and self-regulated teaching environments. The findings gave reflection to the teachers on several vitally necessary conditions enabling a course in a flipped teaching with CALL format to contribute to developing students' professional competencies.