This study aimed to assess the effectiveness of the Mother- Tongue Based Multilingual Education to the indigenous peoples’ learners in Palawan. Indigenous peoples’ learners and their teachers were the respondents of the study. Mean, frequency counts, percentages, Pearson moment correlation, t-test and ANOVA were the statistical tools employed in this study. Most of the grade three learner were in the appropriate age for their grade level, male, belong to big families, spoke Palaw’an at home, belong to Palaw’an ethnic tribe, lived in highlands, live with the core members of the family with large households, and were less privileged. Pupils’ level of academic performance in the core subjects using the three different mediums of instruction did not meet expectation. Teachers had difficulty in dealing with learners’ individual differences, interest and needs as well as integrating MTBMLE to other subjects. The academic performance of the learners was not influenced by their demographic profile except for gender. The learners’ academic performance in Science and Mathematics was influenced by the medium of instruction while the level of academic performance of the learners in the Language subjects was not influenced by the medium of instruction except for mother tongue.