Students’ anxiety due to the COVID-19 pandemic was expressed by some medical students in the form of anger and mistrust. This study aims to explore the reasons for mistrust between students and faculty among medical schools in Egypt that have flared during the COVID-19 pandemic. This is a three-phase exploratory qualitative study depending on thematic emergence from appreciative interviews (AI) sessions. Students are revealed to be very well-educated regarding contemporary medical education concepts. The most important factors from the student perspective were the presence of a well-designed assessment system aligned with the learning outcomes and teaching methodologies and the presence of extracurricular activities and soft skills, respectively. A balanced student life respecting their mental health was found important to increase trust. A roadmap to breaking the mistrust must be planned on several pivots: curriculum structure, extracurricular life, communication strategies, and identifying student roles in their learning and in decision making.