Science|Environment|Health (S|E|H) is a new science pedagogy that aims at promoting the mutual benefit between the three educational fields of science education, environmental education, and health education. Holism and its conceptualisation have become an important topic in recent S|E|H work. In this paper, featuring the invited symposium of the ESERA special interest group 4 at the ESERA conference 2021, we suggest the concept of Two-Eyed Seeing as a basis for the definition of scientific holism in S|E|H. Two-Eyed Seeing as a metaphor was introduced by science education researchers working with Canadian Indigenous citizens. Based on Sellars’s concept of stereoscopic view, we conceptualise Two-Eyed Seeing in S|E|H through an ontological framework. We define scientific holism as the “eye switch” from the scientific image to students’ life-world image, a transition that we consider as equally important as the – more common – reductionist “eye switch” from students’ life-worlds back to the scientific image. Two-Eyed Seeing may then be understood as a continuous circulation of repeated “eye switches” between life-world image and scientific image. We illustrate this approach through three symposium contributions – communicating the meta-organism in school, scientific holism against eco- and health depression, and a holistic visual tool to approach S|E|H competencies – and we discuss consequences for teaching and research in science education. Finally, we point out that, in a new S|E|H pedagogy and beyond, Two-Eyed Seeing may be a helpful extension to the well-established socio-scientific issues approach. © 2023, The Author(s), under exclusive license to Springer Nature Switzerland AG.