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Microscopes are instruments usually associated with the field of Science Education. Unfortunately, despite their great potential for education, their use at school is not generalised. This implies fewer opportunities for students to understand the microscopic world, thus affecting the quality of their Environmental Education. In the present systematic literature review, proposals for Primary and Secondary (6–18 years) microscopy education are analysed, as well as their relation to the promotion of Sustainable Development Goals (SDGs). It has been carried out in the databases Web of Science and Scopus, followed by a content analysis of 82 journal articles. The main results show that non-formal educational contexts pay more attention to the relation between school microscopy and the SDGs than the formal ones, and, within these, basic education is the least represented in comparison to middle and high levels. Optical microscopes are the most used in relation to SDGs, in contrast to electron microscopes, while new digital, virtual and remote-controlled models are also mentioned. Within the Science and Technology fields associated with SDGs through school microscopy, ‘Life Sciences’ and ‘Technological Sciences’ stand out, and these fields are particularly varied in the case of SDG4 (Quality Education) and SDG3 (Good health and well-being). In conclusion, microscopes play a diverse and conspicuous role in promoting SDGs in school contexts at an international level, and their use should be encouraged in Environmental Education formal and non-formal Primary and Secondary Education.