Numerous studies have shown that a considerable number of students do not accept the theory of evolution, prompting the scientific community to seek ways to improve how lessons on evolution are designed in order to promote students' acceptance. A crucial factor identified in many studies is students' comprehension of the nature of science and their perceived conflict between religious beliefs and evolution. Our research aimed to investigate the effects of philosophical dialogues on evolution acceptance, with a specific focus on the relationship between religion and science. We conducted an intervention study in 21 high-school classes in Switzerland. Our findings suggest that high-quality philosophical dialogues can enhance students' acceptance of evolution by addressing the perceived conflict between it and religious beliefs. Conversely, low-quality dialogues may intensify the influence of religiosity, negatively affecting evolution acceptance. Our study underscores both the importance of applying philosophical methods skilfully and the potential benefits of incorporating philosophical dialogues into teaching practices. It also highlights the value of fostering a nuanced understanding of the interplay between religion and science in the context of evolution education.