Student engagement in online learning enhance students performance and the outcomes of the learning process in online learning environment. The existed literature revealed various factors influencing student engagement in online leaning, however these studies were before the COVID-19 crisis. The purpose of the current paper is to explore the factors that influence student engagement in online learning during the COVID-19 crisis in middle school settings in developing countries where is a lack of studies about the factors influencing student’s engagement in emergency remote learning during the crisis. A qualitative approach was used for data collection and analysis. Semi-structured interviews with 34 participants (14 students, 13 teachers, and 7 parents) were conducted for 20–30 min. Furthermore, online class observations were used for data collection; 13 online classes were observed. Each class was 40 min. A thematic analysis was used to categorize the findings into themes and subthemes. The findings of the study revealed that various factors influence student engagement in online learning during the crisis including infrastructure factors, cultural factors, digital inequality, and the threat to digital privacy. Cultural factors were the important factor that influences females because of parents’ culture and their bias against females using online learning compared to male students. Teachers’ presence and quality of content were the major factors that influence student engagement, where parental concerns, norms, and traditions emerged as the major factors in the crisis, influencing engagement. Most of the participants reported that teaching and learning online during the crisis has broadened the digital inequality and threatened their digital privacy which influenced negatively student engagement. The limitations of this research included the limited number of participants covering a large geographic area, and the research design using diverse and often limited educational software and delivery methods. Future studies could utilize a mixed-method approach and include more participants.