The "Vision and Change" report provides a nationally agreed upon framework of core concepts that undergraduate biology students should master by graduation. While identifying these concepts was an important first step, departments also need ways to measure the extent to which students understand these concepts. Here, we present the General Biology--Measuring Achievement and Progression in Science (GenBio-MAPS) assessment as a tool to measure student understanding of the core concepts at key time points in a biology degree program. Data from more than 5000 students at 20 institutions reveal that this instrument distinguishes students at different stages of the curriculum, with an upward trend of increased performance at later time points. Despite this trend, we identify several concepts that advanced students find challenging. Linear mixed-effects models reveal that gender, race/ethnicity, English-language status, and first-generation status predict overall performance and that different institutions show distinct performance profiles across time points. GenBio-MAPS represents the first programmatic assessment for general biology programs that spans the breadth of biology and aligns with the "Vision and Change" core concepts. This instrument provides a needed tool to help departments monitor student learning and guide curricular transformation centered on the teaching of core concepts.