Should I Sterilize Compost Before Use?

If you’ve had problems with plant diseases, you may think putting compost in the oven or microwave is a quick fix cure. Sterile means pathogen-free, right? Well, things are a bit more complicated than that. Former organic farmer and soil expert Logan Hailey explains the nuances of home-sterilizing compost and the science behind pathogen-free compost.

sterilize compost. Close-up of a man's hand pouring a pile of compost from his palm against a blurred green background. Compost, the end product of the decomposition process in a compost pile, is characterized by its dark, crumbly texture and earthy aroma. Compost is composed of decomposed organic matter such as kitchen scraps, yard waste, and plant material, broken down by microorganisms and other decomposers over time.


Gardeners across the internet have shared strange methods for sterilizing soil, from baking it in the oven to steaming it in a pressure cooker to even microwaving their compost. If you’ve had problems with plant diseases, you may think this sounds like a quick-fix cure. Sterile means pathogen-free, right? Well, things are a bit more complicated than that. 

If you’re wondering whether you should sterilize compost, here is the real science of sterilizing or pasteurizing and why we don’t recommend it. Nature has far better tricks for keeping seedlings healthy.

The Short Answer

Compost pile full of aerobic microorganisms. Close-up of a large compost pile in the garden. The compost pile is a mound or heap of organic material, characterized by its earthy, textured appearance and rich, dark color.
Heat-sterilizing harms beneficial microbes.

Heat-sterilizing compost is not recommended for home gardens. It is far better to make or source quality aged compost and blend your own seed-starting mix each time you start new seeds. Sterilizing not only kills the important soil microbes that help plants grow, but research shows that overheating soil can cause phytotoxicity that prevents germination and kills young plants.

Quality compost is already exposed to high temperatures resulting from the aerobic decomposition processes of bacteria and fungi as they break down organic material like food scraps, manure, and leaves. The only reasons for concern about sterility are if you know the batch is contaminated by raw manure or a nearby plant disease (such as mildew-infected leaves that fell near the storage area). 

Sterilized soil blends are often used in the nursery industry to prevent seedling diseases in a commercial setting with thousands of greenhouse plants. While sanitation is important for plant propagation at any scale, sterilizing could do more harm than good. Compost is full of beneficial microbes that help plants thrive and even protect them from diseases. You can think of them as an external underground immune system and digestive system, similar to the beneficial bacteria in your gut. 

Nature does not operate in a sterile environment. Save yourself from the kitchen mess and instead focus on honing your compost skills.

Here are two much simpler preventative measures to keep plant diseases out of your greenhouse or seed-starting area:

Quick Fix #1: Never reuse old potting soil for seed-starting mix. Toss that soil in the garden and create a fresh blend. If you keep a bag of store-bought potting mix on hand, only use a small amount at a time to prepare the seed-starting materials you are starting at the moment. If you ever have a batch of seedlings that succumb to damping off or another disease, throw the old mix in the bushes rather than reusing it for more seeds. Many seedling diseases are caused by overwatering, poor drainage, and a lack of airflow. Conscious irrigation and well-aerated mixes (with perlite, vermiculite, or peat moss) are a great way to prevent issues. Always start seeds in containers with large drainage holes at the bottom, such as Epic 6-Cell Trays.

Quick Fix #2: Source quality compost or make your own with the right ratio of “browns” to “greens. A ratio of 4 parts carbon-rich material to every 1 part nitrogen-rich material is a good place to start. Turn it and use a thermometer to ensure it heats up to above 140-160°F (60-71°C) to kill any disease-causing bacteria or fungi. Once it cools down and ages, this compost will be rich in beneficial microbes without any of the bad ones.

The Long Answer

Close-up of adding organic fertilizer under a young tree in a sunny garden. A large garden shovel is filled with wet compost. Compost has a soil-like texture, dark black in color with moist clumps.
Quality compost teems with life, enriching the soil and aiding plant growth.

Compost is one of the most important garden amendments. From worms to spiders to microscopic bacteria, quality compost should be teeming with life. It enriches the soil with a loamy texture, improved drainage, better water-holding capacity, and billions of beneficial microorganisms that help plants grow. 

Symbiotic soil bacteria, fungi, and other microbes are integral to fueling nutrient cycling so plants can uptake minerals. These invisible organisms also act like an underground immune system, protecting plants from harmful pathogens. Let’s dig deeper into the science of compost dynamics in soil and why sterilizing it could do more harm than good. Plus, we’ll cover the rare occasions when sterilization may be necessary.

High-Temperature Composting is Better Than Sterilization

Close-up of a thermometer stuck into the compost. The compost thermometer is a long, slender tool characterized by its probe-like design and clear, easy-to-read temperature gauge. It has protective casing with a clear display window, allowing users to monitor the internal temperature of the compost pile accurately.
The high temperatures reached in the compost process naturally kill pathogens.

There is no need to stick your compost in a kitchen oven or microwave if it reached sufficient temperatures during production. High-temperature composting uses the natural processes of decomposer microorganisms to break down organic materials, which generates heat. Any compost producer already monitored the temperatures of their pile to ensure they rose to a sufficient temperature to kill off any pathogens. If you make it at home, you can use a thermometer probe to check the temperatures periodically. 

When a compost pile reaches certain temperatures, it naturally kills off harmful organisms, so you don’t have to sterilize it. According to Cornell University:

  • Temperatures above 130°F (54°C) kill the majority of harmful fungi and bacteria but spare beneficial microbes. This temperature also kills weed seeds.
  • In many state regulations, a pile must remain at 130°F for three days to kill pathogens and meet legal requirements for sale.
  • Temperatures above 140°F (60°C) kill tougher weed seeds and viruses.
  • At temperatures over 160°F (71°C), the compost fully sterilizes itself and even kills beneficial microorganisms.
  • Ideally, composters do not allow the pile to get over 140°F. If it gets close to this temperature, cool it by flipping and turning it. 

Composting works by combining biodegradable materials like food scraps, leaves, straw, manure, and grass clippings in a specific ratio, maintaining proper airflow and moisture as microbes get to work. In the process, they release heat, which accelerates the breakdown. 

The pile rapidly warms to 90-100°F (32-38°C). At peak composting, the pile should be 130°F (54°C) for several days. This is when harmful pathogens (for example, E. coli from animal manure) are killed. Any seed-harming organisms are killed at these temperatures as well. 

Only Sterilize if You Know It is Contaminated

Close-up of a homemade wooden compost bin full of compost in the garden. The compost pile is a mound of organic materials characterized by its layered appearance and earthy colors. The pile has a crumbly texture and dark, rich color, indicating the transformation of organic matter into nutrient-rich compost.
Sterilize compost only if contaminated with raw waste or plant pathogens.

The only time home sterilization of compost makes sense is if you know it has been contaminated with raw waste or a plant pathogen like Pythium, which can cause damping off disease in seedlings. Raw manure is usually the culprit of contamination, but raw meat, fish, rotting eggs, or diseased plant materials from the garden could also contaminate it. 

Before you sterilize your compost, make sure to differentiate between unfinished and contaminated compost:

  • Unfinished compost won’t have the classic loamy, crumbly texture and may still have chunks of food scraps or debris in it. In this case, it’s best to compost it again and monitor the temperature. The original ingredients should be indistinguishable in the finished compost.
  • Contaminated compost may have a foul smell, a green slime of algal growth, or powdery spores on the surface. If you notice diseased plants growing near your bin or pile, sterilize it or re-compost the material, ensuring temperatures reach above 130°F (54°C).

Fortunately, contamination is easy to avoid:

  • Never compost diseased plant parts. Instead, burn them or throw them away.
  • Always keep finished aged compost away from areas where you collect ingredients like manure and food scraps.
  • Do not mix raw manure in with finished compost or any potting soil blend.
  • Do not allow infected plants to grow near your pile, or they could blow pathogenic spores into the compost.
  • If a tray of seedlings succumbs to damping off disease, dispose of the soil away from your garden. Do not compost it.

If you know the compost was contaminated, here’s how to sterilize it:

  • Preheat your oven to 200°F (93°C).
  • Place about 4” deep of compost or potting soil in a deep baking tray.
  • Cover with tin foil.
  • Poke a meat thermometer through the foil in the center of the tray, burying in the compost.
  • Put the pan in the oven for about 30 minutes.
  • Wait until the thermometer reads 160°F (71°C)
  • Remove and let cool. Your compost is now sterilized dirt.
  • Thoroughly clean your kitchen.

As you can tell, this could be a messy process. Keep in mind that sterilized soil will not provide the majority of benefits that compost usually does. It will only function as an inert, lifeless medium for germinating seeds, similar to vermiculite or sand, but with more water-holding capacity.

Sterilization Kills the Good Guys, Too

One of the most important benefits of using compost in the garden is its ability to inoculate your soil and your plants with healthy microbes. Sterilization with heat or chemicals basically kills all the helpful inoculants that could have helped your plants. Sterilizing doesn’t only kill the “bad guys’,” it can knock out the “good guy” microbes, too. Those beneficial organisms actually protect your plants from “bad guy” disease-causing organisms. 

Beneficial Microbes Protect Plants from Attack

Close-up of adding vermicompost to young lettuce seedlings in the garden with a blurred background. A gardener holds a garden trowel full of compost over a bed of lettuce. The lettuce plant forms a rosette of oval, oblong, bright green leaves with slightly jagged edges.
Beneficial microbes protect plants from diseases.

Imagine beneficial microbes as an army protecting your plants’ tissues from invasion. In a healthy ecosystem, this microbial army would cover all the surfaces of the roots, stems, and leaves. They are like a living protective barrier enshrining your plants. 

Let’s say a powdery mildew fungal spore flies in on the wind. If that spore lands on a plant growing in healthy compost-rich soil with a strong microbial army, the “good guys” can quickly devour it or outcompete it. But if the mildew spore lands at the base of a plant growing in sterile, lifeless soil, it is more likely to settle in and replicate, causing an infection. It’s easy for invaders to take hold of the plant when there is no army to protect it. This is why sterilization could actually do more harm than good.

Research shows that when a plant is under stress or attack, it recruits protective microbes to improve its immunity and fight against the pathogen. In other words, tremendous microbial battles are happening in our plants and soil at all times. If you want your garden crops to win against destructive plant diseases, don’t sterilize your soil or your compost! You need the “good guy” army on your team.

Understanding the Soil Microbiome

Close-up of a man's hand touching a compost full of microorganisms. The man is wearing a blue sweater. Compost has an earthy texture and dark brown color.
Un-sterilized compost enhances beneficial soil microbes.

Let’s dig a little deeper into the amazing world of the soil microbiome and why un-sterilized, natural compost is an important way to enhance the beneficial microbial communities. A microbiome is a collective community of all microorganisms, including bacteria, fungi, viruses, and protozoa, that live on and inside an organism. Every natural part of the Earth has its own microbiome. In humans, we are most familiar with the gut microbiome, which makes digestion of food possible. 

But there are tons of other microbial communities in our bodies as well, from our lung microbiome to our skin microbiome to your eyelash microbiome (yes, microbes live there, and many of them protect your eyeballs!) Clearly, the types of microbes living in your gut are far different from those living on your eyelashes. In the same way, a plant’s leaf microbiome is far different from the root microbiome (sometimes called the rhizosphere or root zone). 

Modern society places a lot of emphasis on pathogenic microorganisms like E. coli in food or Phytophthora in plants. It is true that these “bad guy” microbes can do a lot of harm. However, the vast majority of bacteria and fungi are beneficial and often essential for life on Earth. 

In the soil microbiome, beneficial organisms help plants grow with essential activities such as:

  • Nitrogen fixation to transform nitrogen into plant-available form
  • Mineralization of rocks to improve the availability of micronutrients
  • Improving soil water dynamics (for example, fungal mycelial networks can improve aeration and drainage)
  • Guarding plant roots from infection by pathogens
  • Breaking down decaying plant matter like leaves and straw
  • Decomposing organic fertilizers so they slow-release into plant root systems

If you want to reap these rewards and more to create a self-sustaining garden ecosystem, it is important to nurture the soil microbiome rather than destroy it! Add unsterilized healthy compost, practice reduced tillage techniques, and avoid synthetic chemicals that may kill off beneficial organisms.

Final Thoughts

Generally, the sterility of compost for a home gardener is not a concern. The decomposer organisms in a pile naturally raise the temperature high enough to kill off harmful organisms. Most commercially produced compost was carefully monitored for temperatures above 130°F (54°C). If you make your own and you don’t think it is “cooked” enough, you may wish to sterilize it in your kitchen

However, beware that sterilizing removes the “good guys,” too, essentially turning it into inert dirt. While this can be fine for growing seedlings (especially if you’ve had issues with damping off disease), it is not ideal for organic gardeners. Quality unsterilized compost is an important source of beneficial soil microorganisms in the garden. 

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