In the institutionalization of the mother tongue-based multilingual education (MTB-MLE) in the country, several trainings were conducted introducing its unique features such as the use of the two-track method in teaching reading based on the frequency of the sounds of the first language (L1). This study attempted to find out how the accuracy track method worked with Waray pupils using mixed vocabularies. This is a part of a developmental study that aims to improve Waray reading instruction in basic education. The researcher used a checklist of the 100 Most Common Words in Waray for pretest and posttest, interviews, survey questionnaires, and daily observations during the three-week implementation of the method. The averages of the pretest and posttest scores were compared. Themes and patterns in the responses were likewise analyzed. The results showed a big gap in the performance of pupils classified as readers and beginning readers. Several issues and challenges met were also identified. These imply that the method is less facilitative for effective teaching and learning in Waray of speakers using mixed vocabularies. This study recommends to modify the method or to develop an appropriate method for literacy instruction of speakers without a strong linguistic foundation in their mother tongue.