Understanding the challenges and preferences perceived by learners is crucial in helping institutions devise strategies to support the continuum of learning during the COVID-19 pandemic. This study used photovoice to examine the barriers in the online learning engagement in chemistry of junior high school students in the lens of their experiences in the online education during the health crisis. The inquiry uncovered four themes: difficulty in understanding the nature of chemistry as a subject matter; lack of intrinsic motivation towards online learning; difficulty in accommodating academic responsibilities in an online platform; and technical challenges associated with online learning. As a participatory mode of research, the students were engaged in a root cause analysis through focus group discussion to account for the causes of their challenges and their perceived solutions to the factors identified. The utilization of photovoice as the platform of inquiry was able to capture the chemistry learning experiences of students and the barriers that hinder their optimum engagement.