In recent years, major drivers of undergraduate science education reform including the National Science Foundation (NSF) and the Howard Hughes Medical Institute (HHMI) have called on college and university instructors to take a more scientific approach to their teaching. Although many biochemistry instructors are gaining confidence in using small-scale formative assessment projects, few have the expertise to conduct more formalized, quantitative studies. And yet this type of assessment project, often associated with the growing field of chemical education research, can be very helpful in gaining greater understanding of student learning and in communicating to peers about new teaching practices and their effect on student learning. This article describes a project designed to improve and disseminate process-oriented guided inquiry learning (POGIL) materials for the biochemistry classroom. To fulfill assessment expectations the author and her colleague have worked closely with chemical education researchers involved in the POGIL project and developed an assessment instrument to identify incorrect ideas students bring from general chemistry and biology to biochemistry courses and to measure changes in student understanding after completing biochemistry.