Processes that transform carbon (e.g., photosynthesis) play a prominent role in college biology courses. Our goals were to learn about student reasoning related to these processes and provide faculty with tools for instruction and assessment. We created a framework illustrating how carbon-transforming processes can be related to one another during instruction by explicitly teaching students to employ principle-based reasoning—using, for example, laws of conservation of energy and matter. Frameworks such as ours may improve biology instruction more effectively than a strategy of cataloging alternate conceptions and addressing them individually. We created four sets of diagnostic question clusters to help faculty at 13 US universities assess students' understanding of carbon-transforming processes from atomic-molecular through ecosystem scales. The percentage of students using principle-based reasoning more than doubled from 12% to 27% after instruction, but 50% of students still poorly used principle-based reasoning in their responses, and 16% exhibited informal reasoning with no attempt to trace matter or energy.