Research studies over the past 30 years have found that individuals have a limited understanding of the theory of evolution and the mechanisms involved in species change. One possible avenue of improvement has been the use of alternative instructional methods, such as inquiry-based activities and teaching about nature of science. Using recommendations from research, this study integrated nature of science, evolution, and inquiry-based instruction to discern its impact on student understanding of evolution. An instructional unit was developed with a community college instructor and carried out in two introductory biology classes with a total of 38 participants. One class was taught using inquiry-based methods, with an integrated approach to nature of science and evolution, while the other was not. Data collection included student and instructor interviews, surveys, pre and post assessments, classroom observations, and student work products. The number of students holding accurate conceptions of the nature of science in the inquiry class was higher for all the reported categories on the posttest. Despite less direct exposure to evolution concepts in lecture, the inquiry class had higher means on two separate posttests for evolution. The traditional class performed better on the pretests yet the inquiry class had higher posttest scores on both measures. Students in the inquiry class held a positive view of the inquiry-based methods and they cited them as a reason for their understanding of evolution. Individuals indicated that the integration of nature of science and evolution allowed them to grasp the concepts of evolution better than if evolution was taught alone. A creationist student became more accepting of evolution and also improved her understanding of evolution. Another student interviewed four years after the intervention remembered only the inquiry-based unit and was able to still use examples from class to explain natural selection. The instructor had a positive view of many of the instructional interventions and integrated them into her course after the study. Four years after the study she has continued to use inquiry-based methods. A number of implications for evolution instruction and future research areas are explored.