This study examines the improvement of first-year students' critical thinking and self-regulation by implementing a metacognitive-based e-module. To address the challenges of learning in accordance with the demands of the higher education curriculum, metacognitive-based e-modules are required. Metacognitive strategies such as analogies, concept maps, mnemonics, and discrepant events integrated into e-modules encourage students to be more critical and independent when understanding concepts and solving problems. The study employed quasi-experimental with two groups, a study group (instructed metacognitive-based e-module) control group (conventional module). Eighty-three students as respondents were involved. The descriptive results indicate that cognitive strategies promote curiosity, facilitate understanding, and aid in long-term memory. Metacognitive-based e-modules could encourage awareness, learning activities, evaluation and interpersonal skills. There is a significant difference in students' ability to think critically and self-regulation. The metacognitive strategy using e-module was found to be stimulating, thought-provoking, and facilitating students to have critical thinking and self-regulation.