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The connection between the cognitive and emotional components of comprehension has remained largely unexamined because of a shortage of dependable techniques for assessing feelings and emotions during educational activities. Concentrating on five distinct stages of comprehension—nascent understanding, misunderstanding, confusion, emergent understanding, and deep understanding—this investigation presents an AI-based method to assess subjective comprehension by tracking the physiological activity visible in facial expressions. To examine these stages, 103 individuals worked on 15 riddles in a remote setting while their facial expressions were video recorded. Action units (AUs) for each stage occurrence were quantified utilizing AFFDEX software. Recurring AU configurations linked to each stage were subsequently pinpointed by implementing six supervised machine learning algorithms. Unique AU configurations were identified for all five stages, with gradient boosting machine and random forest models delivering the greatest predictive precision. These outcomes indicate that physiological activity can be utilized to dependably assess comprehension. Furthermore, they propose an innovative methodology for assessing and encouraging comprehension in instructional environments, as well as designing adaptive educational technologies and tailored learning interventions. Future research should investigate how the physiological indicators of comprehension stages simultaneously mirror and impact their related cognitive workflows, alongside the generalizability of these outcomes across varied demographics and educational environments (A suite of AI tools was employed in the development of this paper: (1) ChatGPT4o (for writing clarity and reference checking), (2) Grammarly (for grammar and editorial corrections), and (3) ResearchRabbit (reference management)).