After the substrate preparation is fermented, it can be moved to the mushroom house for shelving. Mechanical methods are generally used for shelving to save labor. The substrate is evenly spread across each shelf to a thickness of about 20 cm. Then, a secondary fermentation process is carried out to further cultivate the actinomycetes, degrade the macromolecular substances in the substrate, and enrich the small molecular compounds, which are easier for the button mushrooms to absorb for growth.
The secondary fermentation can be divided into three stages: the heating stage, the holding temperature stage, and the cooling stage. During the heating stage, after the fermented substrate is shelved in the mushroom house, steam is introduced to gradually raise the temperature to 60–63°C, maintaining it for 10 hours. In the holding temperature stage, after the heating stage ends, the substrate temperature drops to 50°C and is maintained for 4 to 5 days. During this period, fresh air is introduced moderately to expel waste gases. In the cooling stage, after the holding temperature phase, when the substrate temperature drops to 45°C, doors and windows are opened to allow ventilation, rapidly lowering the temperature to below 30°C, marking the end of the secondary fermentation process.
After the secondary fermentation is complete, the substrate moisture content is 60–65%, pH is 7.5–8.5, and the substrate has turned a brownish color. It is uniformly decomposed, elastic, and emits a sweet fragrance without any foul or ammonia smell. The texture is loose.