Abstract Gender segregation in Islamic law, customs and traditions are adherence practice and requirements in Islamic countries. Thus, increasing number of students in the Muslim, Mindanao or, Bangsamoro Autonomous Region in Muslim Mindanao.(BARMM), Philippines is observable that requires understanding classroom dynamics where students majority are Bangsamoro learner. Teachers play a pivotal role in promoting gender equity to ensure the active engagement of all the learners. As part of the classroom management, teachers face the question of how and where to seat their students. This research aimed to examine the extent of implementing Gender Seat Plan of Secondary School teachers among Muslim students of selected Secondary Schools in Maguindanao II Division. It determined the effects of Gender Seat Plan to the class discipline and performance of Muslim Students. The research uses descriptive research design and purposive random sampling technique in distributing survey questionnaire in order to gather information and make its findings from the teacher-respondents. It was found out that Gender Seat Plan Satisfactorily attained class discipline and achieved class performance of the students. It shows also that it promotes respect in the religious belief and traditions of Muslim students. In the analysis of the findings, this seating arrangement does not directly affect the student’s performance. Thus, it implies that in Muslim communities, it is good to separate male and female in the seat plan to preserve their culture and promote awareness of one’s religious beliefs. It is recommended that additional school policies should be formulated by the PTCA related to the implementation of gender seat plan, there must be an orientation given to the students about the benefits they gain from the implementation of the gender seat plan, and teachers may unite to implement the gender seat plan.