We designed an activity-based science curriculum that used Minecraft to support microbiology learning for students enrolled in the Lang Science Program at the American Museum of Natural History (AMNH) in New York City. Minecraft offered an option to consolidate complex science content into digestible activities for modeling concepts and demonstrate student mastery. We will (1) present a background of the course, design processes, and how we used Minecraft in the curriculum, (2) describe the design of the educational Minecraft activities, (3) articulate design issues, adjustments, and constraints, and (4) discuss future changes.