This study examines the impact of a learning design focussed on providing guided autonomy within a virtual makerspace on the spatial thinking, anxiety and learning creativity of participating students. The learning design deployed within the virtual makerspace was consistent with the learning principles espoused by Self-Determination Theory in that it allowed students to develop "autonomy" and make many important decisions in their own learning, created diverse opportunities for the "relatedness" through authentic opportunities to work with others, and ensured a sense of "competence" through the provision of 'just in time' training and support. Through a within-subjects pre-/post-test design, the study showed a significant improvement in spatial reasoning across the cohort (n = 340). The most notable gains were for students with low but not very low pre-test scores before the intervention. Improvements in creativity and anxiety were also reported by students following the program. Given the research showing the importance of spatial reasoning to future success in STEM educational and career trajectories, these results suggest that well designed makerspace learning may be particularly useful in addressing an important learning gap for disadvantaged students.