How To Disinfect Root Rot Soil: Easy Guide

Root rot is caused by fungus and bacteria that proliferate rapidly in moist, dark environments. Disinfecting soil affected by root rot is crucial, as infected soil can damage healthy plants transplanted into that soil. But how can you sterilize soil infected with root rot?

Here are some helpful ways to disinfect root rot soil:

  1. Bake the infected soil in an oven.
  2. Expose the soil to harsh sunlight.
  3. Boil the soil in a large water-filled pot.
  4. Place the infected soil in a microwave.

This article will delve into these disinfection options, making it easy for gardeners to sterilize affected soil for reuse.

1. Bake the Infected Soil in an Oven

Placing infected soil into your kitchen’s oven may seem odd, but an oven’s high-heat environment could be the ideal place to sterilize root rot soil.

How Baking Disinfects Soil

Bacteria can survive at temperatures below 212℉ (100℃), though most strains begin to die when temperatures exceed 149℉ (65℃). When bacteria enter this range, their cell walls break down rapidly, resulting in cellular death. 

Similarly, fungal spores tend to die after reaching temperatures of 160°F (71℃). So while heat won’t destroy fungal spores in the same way it can break apart bacteria, it can render the spores inactive. 

By baking your affected soil at temperatures above these thresholds, you can sterilize it, making it usable for future gardening projects.

How To Use an Oven To Disinfect Root Rot Soil

To disinfect root rot soil in an oven, you’ll need a large baking sheet, aluminum foil, and oven-safe gloves or mitts. 

Once you have all of your materials, follow these steps:

  1. Preheat your oven to 200℉ (93.3℃).
  2. Place the soil into a metal baking sheet with high sides.
  3. Ensure the dirt is spread evenly across the sheet.
  4. Cover the baking sheet with aluminum foil.
  5. Place the soil-filled baking sheet into the oven.
  6. Allow the soil to bake for at least five minutes.
  7. Use oven mitts or heat-safe gloves to remove the dirt carefully.
  8. Allow the soil to cool.

After the soil has cooled completely, you can place it in sterile containers or spread it on a garden bed.

2. Expose the Soil to Harsh Sunlight

Baking a tray of soil isn’t always the most mess-free method of disinfecting root rot soil. Fortunately, you can use natural sunlight to kill bacteria and fungal spores, especially if you live in a dry and sunny environment.

How Sunlight Exposure Disinfects Soil

Sunlight is a form of radiation. This radiation is partially responsible for helping sunbathers tan and can also (rather unfortunately) increase a person’s risk of developing skin cancer.

But this intense ultraviolet (UV) radiation can also cause mutations in bacteria, resulting in cellular death. Therefore, it can also generate heat to kill fungal spores and destroy the protective membrane surrounding their DNA, leading to internal destruction and an inability to reproduce.

Still, you’ll need prolonged exposure to direct sunlight to disinfect root rot soil.

How To Use Sunlight To Disinfect Root Rot Soil

For this method, you’ll need a sunny area and a flat surface (like a large baking sheet or piece of dry plywood). 

Spread the infected soil across this flat, sunny-drenched surface, ensuring that it’s relatively thin (no more than an inch deep). After that, allow it to remain in direct sunlight for at least 15 minutes, preferably longer.

If possible, begin this process in the morning, directly after sunrise. Doing so will allow for maximum sun exposure, increasing the chances that the UV light will kill all bacteria and fungal spores in the soil. 

3. Boil the Soil in a Large Water-Filled Pot

If you’d rather keep the inside of your oven dirt-free, you can choose to boil the infected soil. This method is also a solid option for those living in rainy, high-humid environments with little sunlight. 

How Boiling Water Disinfects Soil

While excessive moisture can cause root rot, boiling water can destroy the bacteria and fungi that cause this condition. But how does this work?

Water boils when it reaches 212℉ (100℃), though it can boil at lower temperatures at higher elevations. As noted earlier in this article, this is the temperature at which bacteria’s cellular walls degrade, resulting in sterilization. 

Still, boiled soil can develop fungal problems if left inside a water-filled pot for an extended period. For this reason, it’s crucial to have a sterile surface prepared for the post-boil drying process. 

A large pan covered in aluminum foil is an affordable and accessible surface for allowing the water in your boiled soil to evaporate. 

However, you can also pour boiling water into a soil-filled container with drainage holes in the bottom. If you choose this method, just be sure you’re working outside (and standing outside of the drainage area).

To learn more, you can read my other article on sterilizing soil with boiling water here: Can You Sterilize Soil With Boiling Water?

How To Use Boiling Water To Disinfect Root Rot Soil

There are two basic ways to use boiling water to disinfect root rot soil. The most effective method is to place soil into a large cooking pot, cover the soil with water, and place the pot onto a medium-heat burner. However, pouring boiling water on the soil is also an option. I’ll go over both of these options below.

Boil Root Rot Soil in a Pot

If you choose this method, you’ll want to use a wooden spoon to stir the water and soil together, ensuring that the bottom of the pot is wet. Otherwise, you could inadvertently end up with burned bits of dirt at the bottom of your pot.

Stirring throughout the boiling process also ensures that all parts of the soil receive a dose of high-heat water. If possible, allow the water-and-soil mixture to boil for thirty minutes before turning off the burner and removing the pot from the heat.

After boiling your soil, you’ll need to drain away any remaining water. You can pour it out into an unused outdoor container with drainage holes, or you can pour it onto a foil-covered pan. 

If you choose the latter option, you’ll want to spread the soil thin (less than an inch deep) for faster drying. Naturally, it’s also best to do this outdoors, where the risk of creating a mess is slightly less.

Of course, this isn’t the only way to disinfect root rot soil using boiling water.

Pour Boiling Water on Root Rot Soil

The smell of boiling soil isn’t the most pleasant kitchen scent, and boiling water on a kitchen range can get messy. For these reasons, you may prefer to pour boiling water onto the soil.

For this method, you’ll want to fill a metal pail or bucket with the affected soil, leaving at least two inches (five centimeters) of space from the top to allow for water. It’s also best to drill small holes into the bottom of this container before boiling the water, as this will allow water to drain away, reducing the risk of reinfection.

All you’ll need to do is pour boiling water over this soil, making sure to move slowly and cover the soil’s surface. This hot water will drain downward, disinfecting the dirt beneath the surface as it progresses.

Naturally, this method is best suited to outdoor environments. Because the water will drain from the bottom of the container, you’ll want to ensure you’re working on soil or sand. You may also want to wear protective footwear and heat-resistant gloves to stay safe.

4. Place the Infected Soil in a Microwave

If you have an old microwave on hand (or you don’t mind cleaning your microwave thoroughly after using it), you can also choose to microwave the infected soil. However, this option can be particularly time-consuming.

After all, most microwaves have circular plates that only accommodate a single dinner-plate-sized load of soil. So, this method may not be the best choice if you’re attempting to sterilize several pounds of infected soil.

However, the microwave method could be the most convenient option for small amounts of soil or for those who live in rainy environments. It’s also a helpful sterilization method for those living in small apartments that lack standard kitchen appliances like ovens or stovetop ranges.

How Microwaves Disinfect Soil

Microwaves work by exciting the water molecules in a substance. This function results in heat! As we’ve established, high-heat environments are ideal for destroying bacteria and fungi. Therefore, microwaves are an excellent way to disinfect root rot soil, especially if you only have a small amount to sterilize.

How to Use a Microwave to Disinfect Soil

If you’d like to sterilize soil in a microwave, follow these steps:

  1. Empty the soil onto a microwave-safe plate.
  2. Cover the soil with a microwave-safe cover.
  3. Select the high-heat setting on the microwave.
  4. Microwave the soil for three to eight minutes.

Though it may seem counterintuitive, you’ll also want to moisten the soil before placing it into the microwave. Because microwaves work by causing water molecules to vibrate, microwaving dry soil can lessen the effectiveness of this method. 

The best way to moisten the soil you’re preparing to microwave is to spritz it with a water-filled spray bottle. Remember, the soil should be damp but not muddy.

It’s also an excellent idea to ensure that the soil you’re placing into the microwave is spread in an even layer about one inch (2.54 centimeters) deep. Not only will this provide even heat exposure, but it’ll also prevent soil from spilling out into your microwave.

However, it’s crucial to note that microwaving soil (particularly potting soil) can create unpleasant smells that permeate your home. If possible, activate a kitchen vent or open a few windows to lessen the intensity of this scent.


The best way to disinfect root rot soil is to use high-heat environments to kill bacteria and fungal spores present in the soil. 

While you could use harsh chemicals to remove the elements causing root rot, these additives can remain in the soil for a long time and contribute to environmental pollution. As such, it’s often far better to:

  • Bake affected soil in an oven.
  • Expose the soil to harsh sunlight.
  • Boil the soil in a water-filled pot.
  • Microwave the soil on high heat settings.

Alexander Picot

Alexander Picot is the principal creator of, a website dedicated to gardening tips. Inspired by his mother’s love of gardening, Alex has a passion for taking care of plants and turning backyards into feel-good places and loves to share his experience with the rest of the world.

Recent Posts