Indonesia has received little attention in the evolution education research community despite being the world’s largest Muslim-majority nation and the third most populous democracy. As such, Indonesia has the potential to test generalizations and shed new light on the ways in which religion, culture, and formal education contribute to evolutionary understanding, reasoning, and acceptance levels. Here, we report on empirical studies of moderately large samples (n > 300) of Indonesian pre-service biology teachers’ understanding, reasoning, and acceptance of Evolution. In the first and second study, we compare American and Indonesian student’s evolutionary reasoning patterns across a range of tasks using written prompts and clinical interviews. In the third study we investigate Indonesian pre-service biology teachers’ acceptance of evolution. Our first and second studies found that Indonesian participants commonly displayed: lower levels of understanding compared to American samples, mixtures of naive and normative concepts in evolutionary explanations, weak cognitive coherence across tasks, and teleological reasoning in explanations of evolutionary change. In the third study, we found that Indonesian participants, like those in other cultures, have greater acceptance of microevolution, followed by lower acceptance of macroevolution and human evolution. Taken together, our studies suggest that cognitive difficulties inherent to thinking about evolution, to a greater extent than cultural and religious influences, are shaping evolutionary reasoning patterns and acceptance levels in Indonesian pre-service biology teachers. This finding is notable given the strong religious nature of Indonesian society and the prominent role of religion in Indonesian formal education.