This study explored the online teaching experiences of the Junior High School teachers through the lens of the Community of Inquiry (CoI) framework by investigating their perceived level of confidence, pedagogical practices and encountered challenges. Employing concurrent-convergent mixed method design, the study included 66 Junior High School teachers who perceived themselves most confident in the aspect of teaching presence, followed by cognitive presence, then social presence. Having CoI as the school's adapted framework in facilitating online instruction, teachers identified CoI teaching strategies that address the challenges and hindrances in the execution of online instruction underscoring the different presences (teaching, social, and cognitive) and raised instructional dilemmas and challenges that hinder its optimum execution. Recommendations were also offered as inputs in the improvement of the existing school policies and practices in the conduct of online teaching and learning.