We collected think-aloud, pre-test, post-test, and motivation data from 43 undergraduates to examine the impact of conceptual scaffolds on the fluctuation of certain motivation constructs and use of self-regulatory processes during learning with hypermedia. Participants were randomly assigned to either the No Scaffolding (NS) or Conceptual Scaffolding (CS) condition. During the experimental session, each participant individually completed a pre-test on the circulatory system, a pre-task motivation questionnaire, one 30-min hypermedia learning task during which they learned about the circulatory system, a motivation questionnaire at three regular intervals during this learning task, a post-test on the circulatory system, and a post-task motivation questionnaire. Results indicated that while participants in both conditions gained declarative knowledge, participants who received conceptual scaffolds during learning demonstrated deeper understanding of the circulatory system on the post-test. In terms of self-regulatory processes, the results indicated that participants in the CS condition used significantly more planning processes during learning than participants in the NS condition. Additionally, participants in both conditions significantly decreased their use of strategies as they progressed through the learning task. Regarding motivation while learning with hypermedia, results indicated that participants in both conditions reported significantly increased levels of interest as they progressed through the learning task. Furthermore, participants in the CS condition reported the task as being easier and putting forth less effort than participants in the NS condition.