Intuitive conceptions based on cognitive biases (teleology, anthropomorphism, and essentialism) often prove helpful in everyday life while simultaneously being problematic in scientific contexts. Nonetheless, students often have intuitive conceptions of scientific topics such as evolution. As potential approaches to enable students to self-regulate their conceptions in the context of evolution, we investigated the effectiveness of two instructional approaches that are based on metacognition and self-regulated learning: (a) a formative criteria-referenced self-assessment of one's conceptions and (b) instruction on conditional metaconceptual knowledge (metacognitive knowledge about why and in which contexts specific conceptions are appropriate or not). We conducted an experimental intervention study using a 2 × 2 factorial (plus an additional control group), pre-post-follow-up-test design in German upper secondary level biology classes (N = 730). The groups that received one or both interventions had higher conceptual knowledge (i.e., used less intuitive conceptions and/or more scientific conceptions) afterward than those whose conceptions were not addressed: The self-assessment resulted in higher use of scientific conceptions; the instruction on conditional metaconceptual knowledge additionally resulted in lower use of intuitive conceptions based on cognitive biases, more reported thought processes relating to inhibition of cognitive biases, and a better ability to identify inappropriate phrasing based on cognitive biases. No effects were found on students' self-reported metaconceptual awareness and regulation. However, the fact that students inhibited their intuitive conceptions in the post-test indicates that they were indeed metaconceptually aware of and self-regulated their conceptions. The results suggest that students can be taught to become aware of the differences between intuitive and scientific conceptions and to regulate the use of their intuitive conceptions in a scientific context.