The study aimed to determine the relationship between teachers challenges in mother tongue-based multilingual education and pupils academic performance and its relationship. The study utilized a descriptive-correlational research design analyzed through mean and standard deviation and Pearson r correlation. A self-made questionnaire was used to gather data, which was validated and inspected through a reliability test with the use of Cronbachs alpha. Average quarterly grades for the School Year 2022–2023 were used to determine the academic performance of the pupils. A total of one hundred teachers from the four (4) schools in the West II district division of Cagayan de Oro City took part in the study. The study revealed that the teaching and learning process and the preparation of learning resources are not significant to the pupils academic performance. It was also found that teachers training and development have a significant relationship with the pupils academic performance. Thus, this study proves that teachers are resilient in dealing with challenges, and this does not hinder them from performing their tasks to provide the quality education that the pupils need.