2 Steps To Properly Clean a Pot After Root Rot

You just threw away a beloved plant whose roots were slimy and smelly and you are now wondering if it is ok to reuse that pot. Short answer: No! It needs to be cleaned and, bad news, water alone is not enough.

As a whole, to be able to reuse a pot after root rot requires cleaning and sterilizing. Cleaning involves removing all dirt and debris adhering to the pot. Sterilizing requires killing all pathogens that remain after the cleaning process.

Freeing your plant containers from harmful microorganisms is easy, does not need special equipment, and does not need to be expensive. In this article, we are going to discuss how to deep clean your plant containers with household items that you might already have.

2 Major Steps To Deep Clean Pots From Root Rot

Whether it’s terracotta, ceramic, or a plastic pot, your plant can die of root rot which is a disease caused by certain types of fungi that thrive on the roots and in an oxygen-depleted environment. This happens when the plant is severely over-watered for a long period of time.

The bad news?

This problem can be transmitted to healthy plants in case the pot used is infected or was host to a plant that died of root rot before.

Ways To Clean A Pot After Root Rot – Infographic

To avoid the root rot fungi (Pythium, Phytophthora, and Rhizoctonia) from infecting a healthy plant through an infected pot it is important to 1) clean and 2) sterilize the plant container. This two-step approach works well with most plant containers made from clay (terracotta or ceramic) and plastic. They will also work for materials recycled into plant containers such as PET bottles or large plastic tubs that store livestock feed.

Before proceeding, do prepare the following:

  • Warm water
  • Pots to be cleaned
  • Old newspapers
  • Clean rags
  • Cleaning agent – you can use any of the following: a) dishwashing detergent, b) household bleach, or c) vinegar. We will specify the amount later.
  • Bucket or your sink – the vessel should be large enough to hold both water and allow the pots to be fully submerged
  • Brush, sponge, or scouring pad – that fits the size of the pots; you can also use an old clean toothbrush to clean every nook and cranny of the pot.
  • Rubber gloves – safety first; protect your hands at all times from caustic substances.

Remember, it is going to be a bit messy, so I would recommend proceeding with this process outside.

1 – Cleaning (in 3 Steps)

Here’s a simple 3-step approach for a proper cleaning.

Empty: Start by emptying all pots to be cleaned with fully gloved hands. Remove loose dirt clinging to the pot with a brush or a scouring pad. To prevent contamination of other surfaces in your garden, pour the dirt onto old newspapers and dispose of them properly.

Solution: Fill a large clean bucket (or your kitchen sink) with any of the following cleaning solutions and mix thoroughly:

  • 9 parts water and 1 part dishwashing detergent, or
  • 4 parts water and 1 part vinegar

Immersion: Fully immerse the pots to soften stubborn dirt. Use your brush, sponge, or scouring pad to remove all of the remaining dirt. Rinse the pots thoroughly.

Note: If you are using the vinegar solution and hear a hissing sound, don’t worry. It’s a sign that the vinegar is doing its job.

The vinegar or the dishwashing detergent will only remove surface dirt but do not kill fungi spores.

2 – Sterilizing

And here are 3 easy steps to eliminate all remaining pathogens.

Bleach solution: Discard the cleaning solution and rinse the tub thoroughly (or use another tub) then mix 9 parts water to 1 part bleach; this is also known as 10% bleach solution.

Soak: Soak the pots in the solution for no more than 30 minutes. You can opt not to rinse plastic pots but since clay pots absorb water, they should be rinsed thoroughly.

Air dry: Leave the pots out in the open upside down without stacking them to dry thoroughly. If you are using small plastic plant containers, you can use clean rags to wipe off excess liquid.

Clean And Sanitize Fabric Pots [4 Easy Steps]

Fabric grow bags are made from a special breathable fabric similar to those used in shopping bags. They have become popular because they drain well thus preventing root rot due to overwatering.

Due to the material it is made of, the cleaning and storing will be different from other types of pots discussed earlier.

Removal: Remove remaining soil and plant root from the pot by gently whacking it on a hard surface or rubbing together places where there’s buildup. This will loosen the dirt and tiny roots clinging to the surface.

Air dry: If the bag is moist, hang and let it dry completely before proceeding to the next step. If needed, repeat step 1 before proceeding to step 3.

Soak: Fill a large tub with 10% bleach solution and soak the bag for 10 to 20 minutes. Rinse the bag thoroughly.

Drying: Hang to dry completely. Do not skip this step, otherwise, mold will grow on the bag which will affect new plants when reusing the container.

My 8 Cleaning and Sterilizing Tips

These tips will make your life easier and will help you overcome some of the most common problems I heard people are complaining about. Such techniques are:

  1. The sprayer
  2. Soak time
  3. No soil contact
  4. Using bleach
  5. Bleach potency
  6. Smell test
  7. Whitish residue on pots
  8. Using heat

The sprayer: If you do not have a big enough bucket to fit your pots, try using a water spray bottle with the same ratio of cleaning agent described earlier. Be sure to wet the entire surface before removing dirt.

Soak time: Do not soak clay pots for more than 30 minutes because they will absorb too much of the cleaning solution making it harder to rinse afterward.

No soil contact: Do not leave your pots to dry on top of soil, grass, or concrete so as not to contaminate them again. A clean drying rack or a clean elevated surface is ideal.

Using bleach: When using bleach, always use the unscented ones. Do your task in a well-ventilated space as bleach has fumes that can irritate the eyes and the respiratory tract when exposed over a long period.

Bleach potency: Be sure to make a fresh solution after an hour has passed as by then, the bleach has lost its potency due to evaporation.

Smell test: To test if bleach is completely gone from a terracotta pot, wet a portion of it and do a smell test. If you smell bleach, rinse the pot again.

Whitish residue: The whitish residue on your clay plant containers is mineral salts that form a crust on the surface as the water dries up after watering the plants. Sometimes, it can happen that after following the steps discussed above, there is still some build-up left on the surface. This video demonstrates how to use baking soda paste to remove those mineral deposits.

Cleaning Terra Cotta Containers

Using heat: Some people boil their terracotta pots or use the oven to sanitize them. In my opinion, this is not good advice as the boiling action of the water may produce cracks on the pot. With the oven, the heat could do the same damage.

Spin dry: When using the washing machine to clean fabric pots, do not spin dry as it could affect the strength of the bag.

Storing Pots After Deep Cleaning

All types of pots should be stored in a place that is free of possible contaminants. Before storing your freshly cleaned plant containers, clean and sanitize your storage area first. This is to ensure that your pots stay clean and pathogen-free for the next planting season.

  • They should be kept separate from all unclean and untreated tools, plant containers, and other garden equipment in a covered bin, box, or shelving unit.
  • You can store clay and plastic pots stacked on top of each other upside down. Do not stack clay pots too high, the ones at the bottom might break from the combined weight bearing down it.
  • Some gardeners thread a piece of long rope through the center hole at the bottom of the pots, stacking them upside down then hanging the pots together on strong hooks.
  • To prevent from breaking during extremely cold weather, store terracotta pots indoors i.e. your shed. Plastic pots can be stored outdoors but if color fading bothers you, place the pots under a shade or in the same place where you store clay pots.
  • Fabric bags can be folded and tucked away in a cabinet.

Disinfecting Garden Tools After Root Rot

After an outbreak of root rot disease, not only all affected pots should be thoroughly cleaned but also all garden tools (spades, trowels, pruning shears, watering cans, gloves, etc) and surfaces you suspect of contamination.

This action will prevent 3 things: a) the disease from spreading further into your garden; b) the disease from infecting your potting soil supply, and c) the pathogens from killing off new plants.

The steps in cleaning garden tools/equipment and surfaces are roughly similar to what was recommended for pots. It starts with removing dirt and grime and then washing or wiping with water/detergent or water/vinegar mix.

For sterilizing, you can use any of the following:

Lysol or a similar product that has .1% alkyl dimethyl benzyl ammonium saccharinate as an active ingredientUse according to product label recommendation
10% Bleach solutionThis is highly corrosive so do not use on tools that need to be sharpened for proper use such as pruning shears. Dip or spray on tools, rinse with clean water, and wipe off excess water afterward.
70-100% isopropyl alcoholUse as a surface wipe or spray. Thoroughly wet the tool or equipment when using it as a spray. Does not need rinsing
10% Trisodium Phosphate solution (TSP)Soak tools in solution for not more than 3 minutes. Use gloves to prevent skin contact.
25% Pine oil solutionSoak tools and wipe with a clean rag afterward.
Disinfectants for garden tool/equipment and how to use them

Reusing Seed Trays Before Starting Seeds

Reusing garden containers is a great way to keep your gardening cost at a minimum. You can reuse seed trays, flats, and other garden containers but before doing that you must thoroughly clean and disinfect those as well.

Sterilize potting soil after root rot?

Root rot does contaminate soil and many gardeners advise discarding the potting soil after an outbreak. However, there are various ways of properly disinfecting soil to kill harmful microorganisms and make the soil reusable. To know more, please head on to our previous post where we discuss how to sterilize potting soil.


  1. With proper disinfection, plant containers and other things that you use in your indoor garden can be reused.
  2. Using the proper ratio, common household items such as dishwashing detergent, vinegar, and bleach plus water are enough to effectively eliminate fungi and other pathogens that are sticking on your pots and other gardening tools/equipment.
  3. Best practices for all types of gardening include regular cleaning and sanitation. This is not only for your plant’s health but for yours as well.

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“Phytosanitary Procedures for BMPs for Producing Clean Nursery Stock, 2.2 and 2.3” by Tedmund J. Swiecki and Elizabeth A. Bernhardt in Phytosphere Research

“Cleaning with Bleach Can Release Harmful Airborne Particles” by Shawn Radcliffe in Healthline

“Disinfecting Your Garden Tools,” by n.a. in University of Florida

“Clean And Disinfect Gardening Tools And Containers,” by Julie Weisenhorn et al in University of Minnesota

“Control of Pythium, Phytophthora and Rhizoctonia in pot and bedding plants” by Tim O’Neill and Kim Green in Horticultural Development Council

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