Biology majors often take introductory biology, chemistry, and physics courses during their first two years of college. The various and sometimes conflicting discourse about and explanations of matter and energy in these courses may contribute to confusion and alternative conceptions (those that differ from scientific consensus) in biology learners. An important area of biology education research—students' alternative conceptions—has produced a lengthy list of alternative conceptions related to students' understanding of matter and energy flow through biological systems through processes such as photosynthesis and cellular respiration. By synthesizing the research literature and conducting interviews of science faculty members, we have identified similarities and differences in matter and energy discourse and teaching in these different science disciplines. This study can help biology instructors recognize and appreciate the ways in which instructors present concepts related to energy and matter in their courses and alter their discourse and teaching practices to promote learning and minimize confusion among their students.