This paper presents a study about augmented-reality-based chemistry learning in a university lecture. Organic chemistry is often perceived as particularly difficult by students because spatial information must be processed in order to understand subject specific concepts and key ideas. To understand typical chemistry-related representations in books or literature, sophisticated mental rotation- and other spatial abilities are needed. Providing an augmented reality (AR) based learning support in the learning setting together with text and pictures is consistent with the idea of multiple external representations and the cognitive theory of multimedia learning. Using multiple external representations has proven to be beneficial for learning success, because different types of representations are processed separately in working memory. Nevertheless, the integration of a new learning medium involves the risk to hinder learning, in case of being not suitable for the learning topic or learning purpose. Therefore, this study investigates how the AR-use affects students’ cognitive load during learning in three different topics of organic chemistry. For this purpose also the usability of AR learning support is considered and the possible reduction of the influence of the mental rotation on learning success will be investigated.