The Philippines performed abysmally in Programme for International Student Assessment (PISA) 2018 science literacy assessment: only 22% of the 7,233 15-year-old Filipino students who participated in PISA achieved the minimum level of competency (Level 2) in science literacy (Organisation for Economic Cooperation and Development [OECD], 2019). This performance in the science assessment places the Philippines near the bottom of the 79 countries and economies that participated in PISA 2018. In a study that used a machine learning approach, we identified 15 variables that identified the poor-performing students in science literacy. These variables can be grouped into four clusters, namely, metacognitive reading strategies, classroom and school experiences, students’ affect and motivation, and their family experiences and learning resources at home. Based on these results, we suggest a number of interventions that can address these non-cognitive variables that predict poor performance in science literacy.