In the two studies presented in this article, we examine the interplay of conceptual change, text comprehension, and eye-movements during reading and develop and test methods suitable for such explorations. In studies 1 and 2, university students (N = 15 and 23) read a text on photosynthesis, explained their reading processes retrospectively cued with their own gaze videos, and answered written pre- and posttests. In Study 1, a case study demonstrated connections between re-readings and high-level cognitive processing. Out of all of the participants' retrospective reports, categories were formed based on the expressions referring to either situation model or textbase construction during reading. In Study 2, conceptual change learners differed from other learner groups in terms of prolonged overall reading time and a relatively high amount of expressing textbase construction at the beginning of the retrospective reporting. The results emphasise the importance of careful construction of the textbase in conceptual change and point to the benefits of complementing the eye tracking with cued retrospective reporting when examining high-level cognitive processes during reading.