The flipped classroom is a relatively new innovation in teaching middle school science; however, students often struggle with taking notes that provide metacognitive cues and reinforce understanding. This paper describes the structure of a flipped middle school life science class and how the Cornell note-taking method has been adapted to provide structure and routinization to note-taking tasks. Lecture Note sheets were designed for students to record keywords, associated notes or models, summary questions, and muddy points/clear points. The note-taking method was guided by the 5 Rs: record, reduce, recite, review, and reflect. Sections were color coded to allow students to identify keywords and functional definitions on the instructional videos while facilitating efficiency. The use of the Lecture Note sheet is illustrated with examples from an instructional unit on modeling photosynthesis and energy transformation, which incorporated disciplinary core ideas, science and engineering practices, and crosscutting concepts. Anecdotal evidence indicated students improved science understanding and were less likely to communicate misconceptions. This model has promise for middle school learners as they take greater ownership of their science learning with an innovative instructional method that promotes critical thinking skills that are transferable to other academic disciplines.