Online learning has been utilized due to the sudden shift taken among educational institutions to continue students’ learning during the COVID-19 pandemic. Three years into the pandemic, universities now offer different modalities of education due to the establishment of online and modular learning modalities. Hence, the intention of students to adapt to online learning despite the availability of traditional learning is underexplored. With the limited availability of face-to-face learning at the near end of the epidemic in the Philippines, this study sought to analyze the factors that influenced behavioral intentions towards continuing online learning modalities. Five hundred students from different universities in the Philippines participated and answered 42 adapted questions in an online survey via Google Forms. Structural equation modeling (SEM) was used in this study, with factors such as an affective latent variable, attitude towards behavior, autonomy, relatedness, competency, expectation, confirmation, satisfaction, and behavioral intention. The study found that attitude towards behavior has the highest positive direct effect on students’ intentions to pursue online learning, followed by expectation and confirmation, satisfaction and behavioral intention, competence and behavioral intention, and the affective variable and satisfaction. The effect of expectations on satisfaction and the affective variable on behavioral intentions was seen to have no significance regarding students’ intentions. This also study integrated expectation–confirmation theory, the theory of planned behavior, and self-determination theory to holistically evaluate students’ intentions to pursue online learning despite the availability of traditional learning. The educational sector can utilize these findings to consider pursuing and offering online learning. Additionally, the study can help future researchers evaluate students’ behavioral intentions concerning online learning.