•Visual thinking (VT) has potential for dealing with recurring problems in CLIL instruction.•Systemic Functional Multimodal Discourse Analysis facilitates identification of VT features.•Implications relevant for the design of printed and e-learning teaching materials. Content and Language Integrated Learning (CLIL) is a dual-focused pedagogical approach in which a foreign language is used for the learning and teaching of both content and language. CLIL specialists have recommended different types of scaffolding techniques, mainly in relation to language use. However, there is increasing interest in multimodal scaffolding techniques involving language in combination with visual resources. Within this context, visual thinking methodology is considered here as a potentially valuable tool for mediating CLIL. Using a Systemic Functional Multimodal Discourse Analysis (SF-MDA) approach, this study aims to identify several features of visual thinking that could help scaffold CLIL in the science classroom. Some strategies are proposed, both to promote acquisition of scientific language and to facilitate the development of content knowledge. The approach is explored in relation to students’ understanding and communication of complex scientific knowledge in a foreign language in upper secondary education.