The Importance of Greenhouse Sanitation and Sterilizing Soil

Updated: October 11, 2019

OK, I get it. Greenhouse sanitation isn’t sexy and cleaning pots on the weekend isn’t your idea of a good time. I understand. I’ve been you, I know what you’re thinking: this stuff only matters in commercial greenhouses, diseases don’t happen to hobbyists. I’m sorry to be the one to say it, but if you don’t keep your greenhouse and everything in it clean, disease can and will strike when you least expect it. So what’s a gardener to do in a small operation? Read on and I’ll walk you through it.

Start out sterile

The best and easiest way to be clean is to start out clean. From the day you set up your greenhouse, if you take care to keep pathogens out you’ll likely never have to deal with the problems they can cause. That means sweeping up regularly, keeping benches as dry as possible, curing puddling water problems and using sterile medium and pots. Washing the walls and ceiling of your structure are regular chores that help prevent fungal spores from taking hold.

In older structures, it may pay to completely tear down your benches and other equipment and clean them well with chlorine bleach or a commercial product like Green-Shield or ZeroTol. These kinds of tear-downs are good for that time between seasons when you’d love to be in the greenhouse, but have nothing in particular to grow. Don’t forget to wash any lighting equipment you’ve got while you’re at it.

If you have old wooden benches or use a wood-framed greenhouse, a fresh coat of paint will give you a clean, new surface—wood and fungal spores are like peas and carrots. If you use a sturdy outdoor-rated semi-gloss paint, you’ll be able to more easily wash the wooden parts of your operation. When your budget allows, replace those benches with perforated plastic or one of many non-reactive metal options, the maintenance will be less and you’ll have an easier time keeping them clean.

Pots, medium and sterilizing soil

It’s probably pretty obvious when I say that soil is dirty, but I feel compelled to stress this fact because soil, garden soil especially, can be incredibly filthy. Don’t ever bring it into the greenhouse. Though it’s likely that your garden dirt is full of good bacteria and other organisms, it’s just as likely there are diseases and pests in that soil. In the greenhouse, always start with sterile growing mediums or mixes and keep them tightly sealed in sterilized plastic containers when they’re not in use. A lot of experts will tell you to never reuse medium, but you can if you make sure it goes into a dedicated container for dirty medium and sterilize it again before use.

Sterilizing soil is touchy business, so before you even begin, have a meat thermometer handy and plan to pay close attention to what’s happening. Also, it smells—really bad—so make sure to pick a day you can leave the windows open because you’ll want to regardless of the outside temperature. Start by spreading your used soil out on a cookie sheet or other large, flat, oven-safe surface, making a layer less than four inches deep. Set your oven to its lowest setting and move the rack to the middle, or use two racks if you have a lot of medium to sterilize.

Carefully watch the temperature in the center part of your soil container. Once it reaches 180 degrees Fahrenheit, start a timer for 30 minutes. Remove your soil as soon as it reaches the 30-minute mark—toxic by-products are produced in some mediums if they’re heated above 200 degrees. Let your soil cool before moving it to a plastic container that has been freshly sterilized with bleach or an agricultural cleaner and allowed to dry fully.

Pots are another sticking point. A lot of gardeners reuse them, and there’s nothing wrong with that unless you fail to clean them. I’m not talking about knocking the dirt out or giving them a good rinse, I mean really clean those bad boys. My dishwasher has a sanitation cycle, so I cheat and run mine through that, much to the chagrin of my husband, who is thoroughly convinced I can’t tell the difference between the kitchen and the garden. If you don’t have a sanitary cycle or you’ve got a pot you’d rather not risk in the dishwasher, soapy bleach water will do a good job if you allow your pots to soak for a half hour. Rinse them good before dropping them into the pool. Dirt makes it harder for cleansers to get into those tiny scratches and pores of many pot materials.

Label, clean, repeat

seedlings in pots by window - greenhouse sanitation

I know everybody says not to reuse gardening stuff. I know they say it and I know we do it. So, if you’re going to do it anyways, do it safely, OK? Keep containers around for used medium and used pots, seal them and keep them clearly labeled if you can’t immediately sterilize the contents of your various containers. Move freshly sterilized medium and pots immediately to sealed containers to help prevent spores and bacteria from colonizing those teeny scratches and cracks that are so hard to keep clean.

Why? What’s the big deal? I can hear you screaming at me through the Internet. Maybe you’re even thinking I’m just a neat freak with a greenhouse. Common problems in greenhouses large and small include impossible to treat fungi like Phytophthora, Fusarium and Verticillium, stubborn bacteria like Erwina and about a zillion different kinds of plant-borne viruses. Even if you’re careful and always quarantine new plants before exposing them to the general population, the reproductive structures of these pathogens can still blow in from outside.

Once inside, once germinated, disease burns through a greenhouse much more quickly than in an outdoor garden. Your best bet at the point when symptoms become obvious is to destroy everything that even looks remotely sick. You really don’t want to do that, so keep your greenhouse clean, OK? Sanitation isn’t sexy, but aggressive plant diseases are even worse. Even those that are treatable like powdery mildew and rust can drive you mad trying to eradicate them from every plant on your bench.

Best Pot – GROWNEER 0.7-Gallon Flexible Nursery Pot

The pot that made it to the top of our list is the GROWNEER 0.7-gallon flexible nursery pot. You can get this flower pot in a pack of 24 or 48, and they do an exceptional job of starting small plants and seedlings in the greenhouse. You get 24 pots and 15 plant labels in the package, which makes it easy to label your plants without having to write on each pot.

Size of the pots:

The size of the pot is smaller and is commonly used for seedlings, small plants, and flowers that won’t grow as big. These pots also work great for flowers and plants that you want to limit the size of.

The container fits 0.7 gallons of soil and material. It is 6.4 inches tall. The top diameter of the opening is 6.3 inches wide. The bottom width is 4.9 inches wide. The top opening of many pots is only 4 inches wide, but a lot of the time, you are left transplanting and re-potting plants that shouldn’t be touched yet. For flowers and plants that grow quickly, having a starter pot that is deeper and wider will allow your plants to grow further without having to transplant them.

The bottom diameter is a perfect size as well. Some pots have much thinner bottom diameters than top diameters, and this causes instability and risk of tipping when moving around the greenhouse. At the same time, some pots have the same diameters of tops and bottoms, which make it extremely difficult to remove plants in an entire ball. With the bottom diameter being smaller, it makes it easy to gently tip the pot and remove the whole root ball with ease.

Ease of use:

Because the pot is made of soft plastic, it makes it easy to clean and easy to use.

Removing plants from the pots is difficult with pots that are anything but plastic. If you’ve ever tried removing a plant from a metal pot or terracotta pot, you know how difficult it can be to remove the plant and root ball in one piece. Having a soft plastic pot makes it flexible enough to remove easily. This pot from Growneer is also lightweight and reusable. Squeeze the pot all you want with no breakage.

The raised rim design makes it easy to handle, stack, and move the pot. The holes at the bottom are large enough to allow for proper drainage and allow your plants to breathe freely. This is extremely important for greenhouses that tend to have higher humidity.

Overall summary:

With a 0.7-gallon pot that has a 6.4-inch opening and 4.9-inch bottom at 6.4 inches tall, it makes for a great pot. Soft plastic makes it lightweight at hard to break, and the entire design of these pots are perfect for any greenhouse.

Runner-Up Pot – Viagrow 5-Gallon Round Nursery Pot

This pot is less of a runner-up and more of a larger alternative. For greenhouses that house plants that grow quickly or that need a larger pot than the 0.7-gallon starter pot, this is the next step up. In this package of pots, you receive a 10-pack of 5-gallon round nursery pots that can be used for your more extensive greenhouse planting needs.

Size of the pots:

The size of the pots are 5 gallons which make this a better pot for your larger growing and planting needs. For flowers and plants that you know are going to grow quickly, use these pots from the start to avoid transplanting and possibly shocking your plants in the process.

The top diameter is about 12 inches across. The base diameter is about 9.5 inches across. The height of these pots is about 11 inches tall. These sizes are perfect for medium-sized plants as well as plants that you don’t want to have to transplant or move too soon.

Having a larger top diameter than the bottom is essential for transplanting with ease. Having pots with the same top and bottom diameters make it challenging to remove the entire root ball in one piece, and many times you are left with the difficult task of having to cut open the pot or adding excessive amounts of water to get the plant roots out of the soil. It’s also beneficial that the base diameter is not too small either. Having too small of a base diameter makes the plant less stable, and larger or taller plants could be at risk of tipping. The ratio between the top and bottom diameters in this pot is perfect.

Ease of use:

Like our number one pick, this pot is also made of soft plastic that is durable yet inexpensive, making for a great pick as well. Being able to squeeze the container without it breaking is essential, and you can reuse this pot over and over again with proper sanitation.

The raised rim design again allows for many benefits. When not in use, you can stack these pots without having them get stuck into each other. Also, you can lift and move the pots with ease.

These pots have thin plastic, which some don’t see as a benefit. However, this thin plastic allows for easy storage, easy filling, and once filled with soil; it will become sturdy and able to use for a very long time.

The bottom holes are sufficient enough for draining. However, if you need to make the holes more prominent, the pots are durable enough to have a slow drill create new holes or make the current holes bigger.

Overall summary:

Overall, this is a great pot. Thin but durable plastic, wide openings, and large enough space to fit medium-sized plants and flowers make this a recommended pot to use for your greenhouse.

Best Soil – Fox Farm Ocean Forest Potting Soil

The number one pick for best soil has to be Fox Farm’s Ocean Forest potting soil. This brand is ahead of the game when it comes to soil and fertilization of plants and flowers, and their classic “Ocean Forest” blend is essential to any planting needs.

What does it contain?

This Fox Farm Ocean Forest blend consists of rich composted forest humus, fish emulsion, bat guano, sphagnum peat moss, Norwegian kelp meals, and Fox Farm’s premium worm castings to encourage healthy root growth.

If you look at the ingredients of other popular soil mixes, you’ll find that they don’t include as many nutrients as Fox Farm does. Your plants need food to survive, and Fox Farm soils provide all the food your plant needs for a more extended amount of time.

Extra benefits and features:

The Ocean Forest blend is PH-adjusted at 6.3 to 6.8. This allows for optimum fertilizer uptake. That means the naturally rich ingredients in the soil create an ideal environment for anything you plant in it. This PH adjustment creates a better living situation for your plants.

Fox Farm soil is recommended by many gardeners and horticulturists across the country. It is 100% natural and grows plants better than any other soil.

When you look at what people have to say about Fox Farm, you’ll understand why it is such a great brand. Even some of the most challenging plants and flowers to take care of are grown with ease because of this soil. This organic soil outlives any other soil on the market.


Fox Farm stands by their products, and market their Ocean Forest soil blend as the most popular soil that they offer. With the premium ingredients and PH-adjusted medium, this soil will help you grow strong and healthy plants from the very start. This soil is definitely on the pricier side compared to almost every other soil on the market, but you can be confident that you are getting a premium product.

Runner-Up Soil – Proven Winners Premium All Purpose Potting Soil

The runner up soil chosen is Proven Winners Premium All Purpose Potting Soil. If you want the same amount of soil for half the price of Fox Farm’s premium blend, this is the best soil to get.

Some people don’t have the budget to spend as much as people do on Fox Farm’s Ocean Blend soil mixture, and for those that don’t want to suffer too much downside, this soil is the way to go. It is highly used and highly rated by gardeners around the world and is from a brand that claims themselves to be, “The #1 Plant Brand.”

What does it contain?

This premium potting soil contains a professional-grade blend. Their premium all-purpose potting soil includes a mixture of 50-60% Canadian sphagnum peat moss, processed softwood bark, perlite, dolomite lime, a controlled-release fertilizer, and a wetting agent.

Although this doesn’t have the unique ingredients that Fox Farm contains, you will find that this brand of potting soil includes much more than other brands of soil. With this soil, you are getting something that will help continue to make your plants thrive.

Extra benefits and features:

The Proven Winners brand claims to have a specially formulated mix that produces vibrant flowers and healthy growth. You can use this soil for planting at the beginning of the planting season, and not have to worry about changing your soil all season long.

Some brands create soil that is either too heavy or too light. Soil that is too light and airy can cause your flowers and plants not to have a substantial enough ground to grow its roots properly. When this happens, your plants may start to tip or droop. Every time you add water to a light soil mix, your plant may move quite a bit, which isn’t healthy.

On the other side of things, having a soil that is too heavy doesn’t do your plants any good, either. Heavy soil mixtures make it difficult for your plant to breathe. On top of that, it becomes challenging for your heavy soil to be able to drain all of the water you use to feed your plants. Your soil may remain damp and swamp-like, creating root rot and other disadvantages to occur.

This soil mixture is a medium-weight mix that combines air porosity and water drainage availability, making this soil an excellent choice.


This soil was designed to improve plant performance. Whether you use this for seedlings, starter plants, or full-grown plants and flowers, you can be confident that this soil will provide your plants with enough nutrients and fertilization for the entire season. Proven Winners is another brand that stands by its products and believes in everything they put into their soil. If you want a soil mix that will take care of your plants all season long but also won’t cost you a whole lot more than your average potting soil, this premium all-purpose potting soil is your best choice.

featured image: Philipp Deus; image 1: pexels

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