The perceptions and definitions of healthy indoor environments have changed significantly throughout architectural history. Today, molecular biology teaches us that microbes play important roles in human health, and that isolation from them puts not only us but also other inhabitants of urban landscapes, at risk. In order to provide an environment that makes honeybees more resilient to environmental changes, we aim for combining the thermal insulation functionality of mycelium materials with bioactive therapeutic properties within beehive constructions. By identifying mycelial fungi’s interactions with nest-related materials, using digital methods to design a hive structure, and engaging in additive manufacturing, we were able to develop a set of methods for designing and fabricating a fully grown hive. We propose two digital methods for modelling 3D scaffolds for micro-super organism co-occupation scenarios: “variable-offset” and “iterative-subtraction”, followed by two inoculation methods for the biofabrication of scaffolded fungal composites. The HIVEOPOLIS project aims to diversify and complexify urban ecological niches to make them more resilient to future game changers such as climate change. The combined functions of mycelium materials have the potential to provide a therapeutic environment for honeybees and, potentially, humans in the future.