This phase follows the assembly of the fruiting block. Here, mycelium begins to permeate the substrate.

The colonization time depends significantly on the initial quantity of mycelium (also depends on the provided temperature and on the mushroom strain itself). Developing mycelium also requires fresh air during this phase because mycelium produces carbon dioxide (CO₂) during growth.

Therefore, the Pod's bag has a 0.2-micron pore size filter to facilitate gas exchange between the interior of the bag and the external environment. This filter prevents pathogens (mold spores, bacteria) from entering the sterile environment where mycelium is growing.

The phase ends when the mycelium has completely colonized the available substrate.