The effect of online argumentation and reflective thinking-based science teaching on sixth-grade students' epistemic cognition, metacognition, and logical thinking was explored in this study. The research was carried out in the 2020-2021 academic year when all teaching was online due to COVID-19. Students in the study sample were mostly from middle-class families. Students were divided into two groups for one semester; one received online argumentation and reflective thinking-based science teaching (experimental group) whereas the other received only online science teaching (control group). The exploratory factor analyses yielded two factors for epistemic cognition and metacognition questionnaires whereas the logical thinking test was found to be unidimensional. According to the results, experimental group students scored higher than control group students in post-test regulation of cognition and logical thinking. In addition, the experimental group developed knowledge of cognition, regulation of cognition, and logical thinking during the intervention. Although the experimental group scored higher than the control group on the set of post-test epistemic cognition factors, this significance did not appear amongst individual factors. As for the implications of this study, elements of distance learning that may have contributed to the development of students' cognitive abilities were discussed.