The aim of the present study was to investigate the effects of prior knowledge and text structure on cognitive processes during comprehension of scientific texts. To investigate the processes online, we used a thinkaloud methodology in Experiment 1 and a reading time methodology in Experiment 2. In both experiments, we obtained offline comprehension measures and measures of individual differences in working memory and need for cognition. Across the two experiments, the results indicated that readers adjust their processing as a function of the interaction between prior knowledge and text structure. In particular, adjustments in the actual processes that take place during reading were observed for readers who had erroneous prior knowledge, but only when they read a text that was structured to explicitly refute this prior knowledge. Furthermore, the results showed that readers' memory for the text was affected by differences in their prior knowledge, independently of text structure. These findings contribute to our understanding of the relation between different factors that are associated with comprehension of scientific texts and have implications for theories of comprehension and conceptual change.