This study sought to examine the factors affecting the Science, Technology, Engineering and Mathematics (STEM) students’ Mathematics performance in a modular distance learning at Notre Dame Village National High School (NDVNHS). In particular, the researcher was interested to determine if these factors had a significant effect on the students’ Pre-Calculus and General Mathematics performance considering the number of hours spent in modular learning. The period covered by the study was during the first semester of the school year 2020-2021. The respondents were all 67 Grade 11 STEM students of NDVNHS. A quantitative research design was utilized particularly using Multivariate Analysis of Covariance (MANCOVA). The findings of the study revealed that majority of the STEM students had a good performance in their Mathematics subjects for the first semester. Also, the factors specifically type of motivation (intrinsic or extrinsic) and support system (parents, siblings, relatives, friends, or classmates) had statistically significant effect on their mathematics performance in the new normal considering the amount of time they spent in learning using modules. Moreover, there were statistically significant differences in both Pre-Calculus and General Mathematics performances between the type of motivation and support system when adjusted for the number of hours spent in modular learning. Based on the findings, the study concluded that the students’ motivation and support system can greatly affect their mathematics performance when controlling for the allocated time in modular learning. Especially in Pre-Calculus and General Mathematics, motivation and support system are important factors in learning using modules. In the new normal education, the students should increase their level of motivation as well as exposure in self-learning and be given full support towards the processes in the modular approach of distance learning.