Due to the COVID-19 situation, fully online flipped learning that combines online asynchronous learning activities followed by online synchronous discussions and tasks emerged as a working instructional model that provides a conducive learning environment. This study examined the extent to which online flipped reading instruction utilizing scaffolding and digital badges improved deep reading skills and reading engagement of EFL university students at Port Said Faculty of Education. Students were provided with online flipped reading instruction delivered via Edmodo and Google Classroom for reading expository texts. Sixty-eight English-majored freshmen at Port Said Faculty of Education participated in this study. A mixed-methods research design was employed with multiple sources of data, including the pre-and post-tests of deep reading comprehension, the reading engagement questionnaire, and the focus group interviews. Findings showed that incorporating scaffolding and digital badges in online flipped reading instruction can be implemented effectively within the context of university education. Besides, the results indicated that the treatment not only improved the participants' deep reading comprehension but also significantly fostered positive collaboration and active engagement. The study is concluded by suggesting future research that targets constructing a meaningful understanding of online learning environment, deep reading comprehension, and reading engagement with implications for pedagogical practice, particularly with EFL learners.