The use of metacognitive prompting to support self-regulated learning is a well-established area of research in education. Despite receiving considerable attention, the precise mechanism of prompting and its effects on the learning process remain unclear, especially in the context of multimedia learning. This study employed a controlled laboratory experimental design to empirically investigate the effects of metacognitive prompting on learning outcomes, considering both text-based and multimedia learning materials. A population of 110 native Czech undergraduate students in the humanities and social sciences participated in the experiment. Contrary to expectations, metacognitive prompting was not identified as a significant predictor of learning outcomes. Post-hoc analysis indicated that the effects of metacognitive prompting depend on various differences in students and their cognitive processing, which may be further influenced by the nature of the learning material. These findings underscore the importance of considering individual differences when designing and implementing metacognitive prompts in multimedia learning, as well as for follow-up research where they should be closely inspected.