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Since the Force Concept Inventory in 1992, many concept inventories have been developed to cover classical scientific fields. However, there is a lack of concept inventories for interdisciplinary fields, such as biophysics. We introduce a Biophysics Concept Inventory Survey (BCIS), a 20-question, multiple-choice survey to measure student gains in biophysical concepts. The BCIS contains 5 question classifications: remember, understand, apply, analyze, and create, as well as question concepts divided into primarily physics or primarily biology questions. We administered the BCIS to 3 cohorts of students over 4 years. Each cohort participated in a 10-week summer Research Experience for Undergraduates (REU) in biophysics. We compared the presurvey (before REU) and postsurvey (after REU) scores to determine the fraction of the maximum possible gain or loss realized. Our analysis of the results suggests that the BCIS shows no biases based on sex or ethnicity. Further, we used the BCIS to show that 69% of the REU participants showed gains in biophysics concepts, with most of the total participant mean of gain occurring at higher levels of Bloom’s taxonomy: create and analyze. Overall, participants obtain slightly higher scores in physics (8% increase) than biology (5% increase) when comparing the pre- and postscores. The coronavirus disease 2019 pandemic allows a splitting of prepandemic and postpandemic cohorts, with the postpandemic cohort showing significantly larger gains than the prepandemic students. These results show that the BCIS, with question classifications and concepts, probes the students’ ability to apply knowledge to various biophysical science topics without underlying biases and enables instructors to obtain answers to important questions about the effectiveness of the educational programs. The BCIS fills a gap for interdisciplinary concept inventories.