Context-based learning (CBL), promoting students' scientific text comprehension, and fostering metacognitive skills, plays an important role in science education. Our study involves CBL through comprehension and analysis of adapted scientific articles. We developed a module which integrates metacognitive prompts for guiding students to monitor their understanding and improve their scientific text comprehension. We investigated the effect of these metacognitive prompts on scientific text comprehension as part of CBL in chemistry. About 670 high school chemistry students were randomly divided into three groups exposed to high- and low-intensity CBL. One of the high-intensity groups was also exposed to metacognitive prompts. Research tools included pre- and post-questionnaires aimed at measuring students' conceptual chemistry understanding and metacognitive knowledge in the context of reading strategies, before and after exposure to the CBL. Chemistry understanding was reflected by students' ability to identify the main subject of the adapted article and by explaining concepts both textually and visually. We found that high-intensity CBL combined with metacognitive prompts improved students' chemistry understanding of the adapted scientific articles and the ability to regulate their learning. Our study establishes that reading context-based adapted scientific articles advances students' conceptual chemistry understanding. These gains are strongly amplified by domain-specific metacognitive prompts.