Muslim students have a high perceived conflict between religion and evolution. For this reason, constructivist teaching was implemented to emphasise the balance of the nature of science (NOS) on evolution and creationism theory within the conceptual ecology for biological evolution (CEBE) framework. This study explored changes in students’ CEBE and how perceived conflict, NOS, and religion contributed to the evolution of acceptance during the course. This research followed a one-group pre-test and post-test design to gather data. Data collection tools used in this study included a questionnaire and a reflective essay. The study group consisted of third-year undergraduate biology students aged 20–22 from Universitas Islam Negeri Maulana Malik Ibrahim Malang in Indonesia. Questionnaire responses were analysed using statistical methods, including paired t-tests, correlation, and hierarchical regression, while reflective essays were analysed using content analysis. The study found that students’ acceptance increased after the course and was correlated with their knowledge, religiosity, understanding of NOS, and perceived impact. The understanding of NOS was the primary factor influencing the acceptance of the theory of evolution, while perceived conflict has the least impact. In addition, reflective essays showed that while most students had a naive knowledge of evolutionary reasoning, they could explain the nature of science. The students were able to establish a complex relationship between science and religion using the chimpanzee-human relationship explanation. This study has provided an example of a learning method to minimise students' perceived conflict in the evolution course.