The gradual shift to online modes of learning in higher education institutions over the past 2 decades accelerated drastically on a global scale between 2020 and 2022. Students and educators, who have initially grappled with the shift, have now become accustomed to online teaching; however, there are concerns about the quality of learning that has resulted. To enable a sustainable and effective online pedagogy, educators may need to learn about fostering higher-order thinking skills, which can be challenging even for experienced educators. To conceptualise effective online pedagogy, the community of inquiry (CoI) framework emphasises cognitive presence (CP), which focuses on the higher-order thinking process. The CoI is the most widely researched framework in online pedagogy, yet contemporary CoI literature lacks collective evidence of factors that influence CP. This scoping review of the CoI literature explores the factors that influence the higher-order thinking that is indicative of CP. Inclusion criteria included evidence of CP in online learning contexts and published between January 2000 and March 2022, providing a total of 121 studies. Results suggest that teaching presence, structure of learning activities and student characteristics all influence CP. Implications for practice or policy: Higher education students enrolled in online courses should be taught how to learn effectively in an online mode. Online course educators must embed learning tasks that foster self-regulation and higher-order skills in students. Online course design should include authentic tasks for students to apply new knowledge to real-life scenarios. Educators must be offered ample professional development activities to build their skills in online pedagogy. Institutions should encourage translation of online educational research to practice.