Sanitizing and Cleaning the Cannabis Grow Room: Part II Plants & Substrate

In Part 1 of this series, we wrote about the importance of grow room sanitation and a regular inspection and cleaning schedule. We also covered ground on the difference between sanitizing, disinfecting, and sterilizing the grow space. In this article, we’ll cover the sanitization of plants and substrates and the ways cultivators can prevent damage and loss to their crop from bacteria, fungi, pests, and plant diseases by cleaning their grow room on a regular basis.

A Preventative Approach

There are many methods to anticipate and treat issues early in the garden. One commonly utilized strategy for keeping plants clean of pests is called Integrated Pest Management (IPM). IPM applies a combination of techniques that are environmentally sound and reduce the need for pesticides.

Preventing pest problems before they arise saves time, money, and possibly the whole crop. The common methods for prevention using IPM include:

  • Creating uninviting environmental conditions in the grow space
  • Increasing sanitization of your cannabis grow room
  • Enabling plant and soil systemic resistance
  • Designing your grow room and airflow properly
  • Use of Beneficial Insects
  • Use of approved pesticides when required

Scouting and tracking for pests are one of the best preventative methods any cultivation facility can employ to get ahead of issues. Cultivators also set up spore traps around their grow rooms that are then lab-tested to identify what molds might be present. The results help guide the operation as to what processes and treatments are needed to sanitize their grow space properly. Accurate identification of pests and pathogens is crucial to deciding the method of treatment response.


The clone room growing environment is a perfect breeding ground for molds and fungus. Clones need humidity and warm temps. In addition, when they’ve first been cut, they are under a lot of stress and can be susceptible to fungus like powdery mildew. Powdery mildew can be challenging to get rid of once it spreads. It is crucial to identify the source in the grow room immediately. If the cultivation facility takes clones from its own mother plants, that is the first place to regularly inspect for early signs. If the mother plant is infected, all clones from it will be too. In this case, starting fresh with new and clean mother plants is the best option.

If your cultivation facility gets clones from a nursery, there are certain precautions that must be followed to prevent issues from entering the cannabis grow rooms. Clones should be inspected for pest and disease issues prior to purchase from nurseries. An easy process to implement in a grow room is thorough sanitizing when bringing clones in from outside the facility. A good practice is to isolate and quarantine the new clones before introducing them to the mother or vegetative production areas. During this time, inspect and treat thoroughly for pests or plant diseases and treat them prior to transitioning.

All tools, equipment, and surfaces must be sterilized thoroughly. Plastics such as pots, trays, and domes should also be cleaned and sterilized prior to use in the clean grow room. 91% or greater Isopropyl alcohol diluted 30% with water is commonly used for tool and surface sanitation. Hydrogen dioxide, hydrogen peroxide, and peroxyacetic acid are commonly used to clean plants and/or surfaces. The frequency between sterilization is up to you. Some growers clean all tools daily while others between plants so as not to spread infection. The level of risk management is a personal decision.


Most growers separate their plants into dedicated cannabis grow rooms based on the plant cycle: mother, clone, veg and flower stages. When designing an indoor vertical grow facility, planning for dedicated, clean grow rooms helps mitigate risk factors plants face. If one room is infected or compromised, the team can fully address and sanitize the individual room without affecting the progress in the other rooms. Some growers choose to keep the mother plants in the same grow room as the veg plants to save on grow space. Most growers keep the mother plants in a designated area separate from veg plants to reduce the risk of cross-contamination (both pest and disease) between older and younger plants.


Just as preparing a sanitized environment is important to preventing crop failure, so is the resetting of your indoor grow room to a neutralized, clean environment that’s ready for its next round. After all the plants have been cut and transferred from the grow room to the drying room, clear all supplies from the area and remove any plant matter from the ground and trays. In addition, clean all surfaces of dried nutrients and plant matter which are food for pathogens and fungi.

Hydrogen peroxide and dioxide solutions as well as other chemical cleaners disinfect the surfaces without leaving any residue while keeping your grow room clean. Ensure the concentration of hydrogen dioxide is safe for handling and always follow the label as directed.

Grow Medium

With the exception of no-till living organic soil practices, the substrate should be new from the packaging and inspected for quality prior to use. Substrates such as rockwool and hydroton are considered to be sterile media in comparison to soil-less hydroponic mixes and soils which can sometimes have unwanted pests, like root aphids, that hitchhike along. In some cases where cultivators are reusing their substrate, growers are disinfecting before using again through methods such as steam sterilization.

Tools of the Trade

There are tried and true modern technologies in the commercial cultivator’s toolkit for growing cannabis and surface sanitization. Post-harvest cleaning with bio-foamers and/or bio-foggers are very effective in treating racking, trays, surfaces and floors. The bio-fogger uses microdroplets that enable you to get into impossible-to-reach nooks and crannies for a deeper level of sanitizing through improved surface contact.

It’s also beneficial to use equipment that is anti-microbial and fungal-resistant like PIPP’s Vertical Grow Racks in conjunction with their Drip-to-Drain or ABS Combination Grow Trays. The trays come with optional HDPE inserts and have a white powder coat finish that is UV-stable and anti-microbial and fungal resistant.

Sanitization Practices

Keeping your grow room clean and tidy is the easiest preventative method. Clean up and remove dead leaves, stems, substrate and water from the floor or and in the grow space. Pests and diseases are looking for homes, so limiting their options is an easy preventative measure. Any plant material that is trimmed off plants must be removed from the grow room after completion of tasks. Green waste and trash should be stored outside the grow room to further ensure a clean growing environment. Tools should be kept off the floor on a workbench or wall. Keep a sanitizing solution of isopropyl alcohol nearby and instruct employees to sterilize the tools before and after use.

In this Part 2 of the Sanitization series, we’ve covered Integrative Pest Management and grow room cleaning best practices for plants and substrates. We’re now ready for the last part of this series. In part 3, we’ll be talking about the sanitization of air and HVAC systems.

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