In this paper, we focus on perceived cognitive presence (CP) in three sections of an intermediate level English for Academic Purposes (EAP) course facilitated online. The researchers intend to demonstrate how lesson design, scaffolding, and a blend of synchronous and asynchronous delivery create perceived CP. Data was collected from the CoI survey (Arbaugh et al., 2008), administered to both student and instructor participants, as well as an analysis of the lesson plans. Focusing on the survey questions related to the four phases of CP, researchers assigned numerical values to responses reported by participants (cf. Arbaugh et al., 2008). Student participants consistently reported lower levels of CP than teachers in the "triggering event" and "exploration" phases. Student participants in two of the three sections also reported "lower" levels of the "integration" and "resolution" phases than the teacher, but students in the third section reported "higher" levels. Moreover, student-reported experiences of CP in all four phases, except the exploration phase, increased with each iteration of the lesson plan. In addition, we analyze the weekly lesson plans in relation to the four phases of CP. Results demonstrate the relationship between lesson plans and perceived CP and will help to inform best practices in online learning contexts.