5 Essential Tips to Prevent Contamination while Cultivating Mushrooms

Mushroom cultivation is a rewarding but delicate process. Contamination can be a grower’s worst nightmare, leading to devastating crop losses, reduced yields, wasted time and resources, and even potential health hazards. However, with the right practices, you can significantly reduce contamination risks and enjoy a successful harvest.

These are 5 practices you can incorporate into your workflow that can minimize contamination risks to promote a successful harvest. This brief guide is tailored for beginner mushroom growers and is particularly suited to those using MycoLogic’s Spore 40 Fruiting Module. However, these principles can be adapted to most mushroom cultivation practices to reduce the risk of contamination.


Prioritize Sterility and Attention to Detail

One of the simplest yet most effective ways to minimize cross-contamination is to maintain good personal hygiene. Using personal protective equipment (PPE) such as masks, gloves, hairnets, beard covers, and shoe covers can help prevent microorganisms from transferring from your body or clothing to the growing environment.

Developing a high attention to detail is also fundamental in maintaining sterility and preventing contamination. During lab work with cultures and sterile substrates, be aware of any sterile tools or surfaces that may have been compromised by touching something non-sterile. If you suspect contamination may have occurred, take immediate action to resterilize or replace the affected tools.

For example, sanitize your gloved hands frequently with an alcohol solution from a spray bottle during procedures, especially after touching non-sterile materials. Replace sterile instruments, such as serological pipettes or scalpel blades, if you suspect they’ve been compromised. Use an open flame or incinerator to periodically sterilize metal tools throughout your work—not just at the beginning and end of a session.

While not all PPE may be necessary for every activity, assess the specific risks in your procedures and use appropriate protective measures for the risk you’re willing to take.

Gloves are a necessity when handling cultures to prevent cross-contamination.

Source Quality Substrates

Using high-quality substrates is critical to successful mushroom cultivation. When sourcing substrates, choose vendors with reliable reviews whenever possible. If you’re preparing your own substrate, prioritize pure, fresh, properly-stored materials that have minimal pesticide exposure.

Sometimes this information isn’t available, so you may need to monitor the performance of substrates from different vendors to identify the best options that work for you. This is where maintaining good record keeping of harvest yields as well as other variables, such as substrate composition and environmental conditions, can pay off by identifying factors that affect performance.

Confluent white mycelial growth of Pleurotus ostreatus (oyster mushroom) across hydrated rye grains is an indicator of healthy colonization.

Inspect Your Growth Substrates

While you can’t always prevent contamination, acting quickly to address it can stop its spread. Regularly inspect your growth substrates for signs of contamination, which can present as discoloration, unusual odors, or atypical fungal growth. If you notice any of these issues, immediately remove the affected substrate to protect the rest of your batch.

Contamination also isn’t limited to the fruiting stage, where your substrate is exposed to the air. Microorganisms can colonize any hydrated organic material used in the process of producing mushrooms. Certain contaminants can even infiltrate through filter patches during the colonization phase and spread between substrates in your colonization space. Vigilance at every stage of growth is crucial.

In the photo below, there’s a large contaminating growth of a blue green fungus, possibly a Trichoderma species. This can be identified by the drastically different color than the bright white mycelia of the Pleurotus ostreatus (pink oyster mushroom) that the substrate block has been colonized by. This block should be carefully removed from the grow space to prevent disturbing the spores and causing them to spread via the air to other blocks and the surrounding area. By the time this dark coloration is visible, there have already been thousands or millions of spores produced by the contaminant. Therefore, it is not recommended to attempt to salvage the block by attempting to control the contamination by applying bleach, burning the area with a flame, cutting the area out, or other methods, as these activities are only likely to disturb the spores, causing them to become airborne and contaminate other materials in the room.

A contaminant growing on the substrate block that’s fruiting pink oyster mushrooms (Pleurotus ostreatus).

In the photo below, there’s a dark contaminating fungus growing at the top of the Petri plate with a Trametes versicolor (turkey tail mushroom) culture. This contaminant can be identified by the much darker colored spores it produces as well as a distinct margin as it grows outward to touch the T. versicolor culture. In this situation, do not open the plate, as it will release the contaminant’s spores into the air. You should discard the plate and try to identify any other materials that were inoculated from this culture and subject them to heightened monitoring for similar-looking contaminating growth.

A contaminant growing over a Trametes versicolor (turkey tail mushroom) culture on agar.

Keep Surfaces and Equipment Clean

Organic debris, such as fallen mushrooms, spore buildup, and substrate, can become breeding grounds for contaminating microorganisms. Contaminants will use this organic material as their own growth substrate, so ensure your growing area—including floors and shelves—is cleaned regularly. Conduct spot checks regularly as a part of your preventative maintenance schedule and promptly remove any organic matter to reduce the risk of contamination.

Buildup of spores on fan blades can both reduce the efficiency of the fan and serve as growth substrate for contaminating molds.

Control Insects

Insects are an often overlooked source of contamination. Not only can they introduce contaminants into your growing environment, but they can also bite and damage mushroom flesh, creating entry points for pathogens. Additionally, insects can quickly lay large amounts of eggs, leading to uncontrollable infestations.

Preventative measures, such as fly traps, can help capture insects before they come into contact with your mushrooms or substrates. A shoe brush can help remove material that may harbor insects or their eggs from making its way into the grow room. Proactively addressing insect control is vital for maintaining a clean growing space.

If you do notice insects colonizing mushrooms or substrate, remove all affected material immediately and clean all surrounding surfaces with a bleach solution. You’ll also need to increase your monitoring efforts to watch for any other substrates beginning to show signs of insects.


By adopting these tips, you can minimize contamination risks and focus on enjoying the fruits of your labor. A proactive approach is always more effective than reactive measures.

Are you seeking a setup that simplifies cleanliness? MycoLogic’s Spore 40 Fruiting Module is your perfect solution. Its bright, all-white interior helps you easily spot and address potential contaminants, while its durable epoxy-coated flooring allows for effortless cleaning through mopping or pressure washing.

Ready to optimize your mushroom growing environment? Discover how the Spore 40 Fruiting Module can provide the ideal conditions for cleanliness and productivity.