This study explored indigenous educational practices of the Ethiopian Orthodox Church Qene Bet education and its implications to the modern educational practices. The study employed a qualitative approach with an ethnographic 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 through field observations, semi-structured interviews and focused group discussion from Yenetas (Qene Teachers) and students. Twenty-four participants have participated in the study. Data is analyzed and results are presented based on thematic approach. The findings indicate that Qene Bet 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, self and peer assessment and scaffolding are central to the Qene education system. The study concluded that Qene Gubae Bet schools pedagogical practices have valuable insights for the current pedagogical practices of contemporary schools in Ethiopia.