Short-answer questions are commonly used for assessment in secondary biology education, but their scope limits what can be observed. If a curriculum intends to encourage students to think deeply about how biological systems function, or to integrate physiology, development, evolution and ecology, then longer-answer assessments are required. This article presents two simple frameworks that can be used for assessing biological thinking beyond short-answer questions over educational stages and different contexts, to complement standardised testing. Additionally, by sharing the frameworks with students, it is postulated that they will understand better how to learn in biology.