This work investigates how ecological literacy and nature connectedness can be fostered in children aged 8–12 through engagement with a toolkit for place-based nature education. Children growing up in urban environments often lack access to nature, leading to lower ecological literacy and feeling less connected to the natural world. To help children reconnect with nature, we propose situating nature education in local environments, facilitated by a toolkit developed through a research-through-design approach that combines methods and perspectives from material-driven, participatory, and more-than-human design. Material explorations and a workshop with primary school children informed the conceptualisation of the toolkit, which invites children to shape mycelium-receptive artefacts, place them in local environments, and observe their transformation over time. Using clay as a substitute material, the shaping and placing activities were tested with 71 primary school children across four classes, alongside imaginative and reflective activities to encourage empathy and sensitivity toward fungi. Findings suggest that the shaping, placing, and reflecting activities can support ecological literacy and caring relationships with non-human organisms, indicating the potential of place-based, more-than-human learning tools to enrich nature education and reconnect children with nature.