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The reasons why and how students often fail to effectively use SRL strategies during learning is not fully understood. Our study aimed to understand underlying structures of strategy deployment by examining the use of system- and learner-initated cognitive and metacognitive SRL processes during learning through PCA of 190 undergraduates learning with MetaTutor, a hypermedia-based intelligent tutoring system. Results showed that the system’s underlying architecture deploys processes corresponding to the phases and type of effort allocation based on Winne’s (2018) theory of SRL. However, learner-initiated processes within the experimental condition only shared the latter. Additionally, learners in both conditions shared a component representing the familiarity of processes. Regression models using these principle components outperformed raw frequency models.