The study explored pedagogical practices of the Ethiopian Orthodox Church Qene Bet education and its implications to modern educational practices. The study employed a qualitative approach with phenomenological design. Three Qene Gubae Bets, one in Bahir Dar City administration and the other two in West Gojjam administrative Zone, were selected using purposive sampling for this study. Data was gathered over a period of eight months through observations, semistructured interviews and focus group discussion with Yenetas and students of the Qene Bets. Observations provided insight into the teaching and learning methods, assessment and evaluation practices, classroom organization and management, teacher student interaction, school environment, daily life of students and ethics and moral cultivation practices in Qene Bet schools. Twenty four participants (three Qene teachers and twenty- one Qene Gubae Bet students) have participated in the study. Data is analyzed and results are presented based on thematic approach. The findings indicate that Qene church schools have their own indigenous pedagogical practices such as Qene ‘Qotera’ (self-study), Qene ‘Negera’ (oral presentation and defense) and Qene ‘Zerefa’ (creating and presenting original Qene poems) that demands student centered and deep learning approaches. The findings also indicate that the practices of cooperative learning, peer learning, reflective learning, pace learning, critical interpretation, argumentative oral defense, differentiated instruction, authentic formative oral assessment,self and peer assessment and scaffolding are central to the Qene education system. Other findings indicate that role modeling, storytelling, guidance and counseling, mentorship, school rules and regulations, students peer counselors were found the most frequent pedagogical approaches in place for moral education in church schools. The study also found lack of food, lack of suitable learning places, lack of residual house, lack of materials, lack of awareness creation about the contributions of Qene Bet education, lack of supported stakeholders as the major challenges facing in Qene Gubae Bets education. The study concluded that Qene Gubae Bet schools pedagogical practices have valuable insights for the pedagogical practices of contemporary schools in Ethiopia.