In this study, we explore the link between children’s agentic virtual making in the digital game Minecraft, and science education and children’s views of nature concerning sustainable development. The research questions are as follows: Which agency do children express in their virtual making in relation to science and sustainable development? The study adopts a qualitative analytical framework based on agency and activity. Three dimensions are discussed: agentic virtual making focusing on body movement (avatars versus real body); context manipulation; and content mixing (knowledge, notions, formal learning, and media content). The findings indicate that Minecraft offers a unique platform for children to connect with nature and develop environmental awareness. Overall, the study underscores the potential of informal virtual making in Minecraft to activate interest and learning in science education, offering educators new avenues for engaging students and addressing misconceptions.