There are multiple examples in the literature highlighting the connection between gestures and meaning‐making by students learning chemical concepts in chemistry; however, there is little known about whether this connection extends to student learning in biochemistry. Moreover, learning biochemistry often involves the use and coordination of multiple external representations (ranging from 2D illustrations and physical models to 3D virtual models) of macromolecules. How does use of these external representations impact student gesture production and meaning‐making when learning new biochemical content? In this study, we used a newly developed augmented reality (AR) model of the KscA channel to investigate the influence of external representations on student produced gestures during a discussion on KscA function. We focused on several research questions: what are the different biochemistry content knowledge that students express through gestures? What are the different types of gestures and patterns of gesture production used by students to express content knowledge? What are the differences, if any, in student produced gestures before and after the introduction of an AR model? What are the relationships between student produced gestures and the AR model? Semi‐structured clinical interviews were conducted and recorded through Zoom. Seven undergraduate students who enrolled in an upper‐division biochemistry course participated in the interview. During the interview, participants were presented with an AR model of KcsA channel after proposing a theory of how potassium ions move through the channel. Participants were then asked to modify their theory. In the first stage of analysis, interview participants’ utterances were transcribed and their gestures were described in terms of hand shape and movement. The identification of unique gestures as part of the coding process highlighted the importance of hand shape vs movement vs a combination of both as ways to delineate different gestures. In the second stage of analysis, qualitative and quantitative differences in student gesture production were identified through a comparative analysis of student gestures before and after their exposure to the AR model. Exposure to the AR model resulted in a shift from gestures that were more general (for example, holding two hands parallel to represent the channel) to more specific to the channel representation they say (for example, holding two hands to form a funnel shape or curling one hand into a tube shape). Our findings add to existing literature on the use of external representation in biochemistry education by highlighting the relationships between AR mediated external representations and gesture mediated external representations. Implications for both the development of new external representations and instructor’s choice of external representations are discussed.