How To Sterilize Your Plant Containers for Seed Starting

Cleaning last year’s growing supplies is a quick step toward preventing disease issues for tender seedlings. Garden expert Katherine Rowe explores easy ways to disinfect pots and containers for reuse this season.

A blue watering can placed next to various black and gray pots of different sizes, with a pair of gardening gloves lying nearby.

Contents

Starting seeds in winter is a rewarding and cost-effective way to get a jumpstart on the spring growing season. Reusing supplies is a benefit of good seed-starting equipment. An initial investment goes a long way for years of use. Reuse also keeps the materials (often difficult to recycle) out of the waste stream. Trays, cell packs, and pots are stored easily in the off-season for handy access come late winter and spring’s round of sowing.

Sanitizing the growing space, equipment, and tools before getting down to seeding is a good early step to accomplish on a winter day. Sterilizing pots and cell packs that house seedlings is a preventative measure against fungal, viral, or bacterial issues carried in the remnants of earlier rounds. We’ll explore quick and easy methods to make the task less of a chore for ready-to-go supplies.

Benefits of Sterilizing Pots

Several terracotta pots submerged in water inside a bright red bucket, with small bubbles and debris floating on the surface.
A quick cleanse gets rid of the buildup for like-new planters.

Pots carried over can harbor remnants of disease-causing pathogens, fungi, and other organisms like insects. They remain in the debris and small particles and can spread to fresh soils and seedlings.

Mineral and salt deposits, too, can impact and dehydrate tender roots and stems. They build up on the soil rim of plastic and clay pots. With clay, they leach and appear on the outside of pots as well. A quick cleanse gets rid of the buildup for like-new planters.

Prevent Damping Off

Green seedlings with broad leaves growing in black trays filled with soil, showing signs of disease.
The stem weakens and can’t support upper growth. Seedlings collapse and die back.

Damping off is a common fungal problem for seedlings, and fresh potting mix and clean supplies are the first steps in prevention. This disease often results from overwatering and soggy conditions, but it can impact seedlings in well-draining situations if carried over in growing supplies. 

Damping off presents with brown stems at the soil level. The stem weakens and can’t support upper growth. Seedlings collapse and die back. Several pathogens like Fusarium, Pythium, and Rhizoctonia cause the condition (we see these in the garden as wilt and rot issues). The fungi spread quickly and impact all seedings in a flat. So, to be on the safe side, a quick sterilization gives the best foundation.

Supplies to Sanitize

A collection of terracotta pots of various sizes, stacked inside a large white pot and arranged nearby on the ground.
From clay to plastic to stone to other materials.

Any previously used growing container is a candidate for sanitizing, from clay to plastic to stone to other materials. Basic seed starting supplies, from indoor setups to alternative techniques like soil blocking and winter sowing, allow for material reuse and benefit from cleaning. Disinfecting hand tools and surfaces, too, gives a fresh start toward plant health.

Indoor starting supplies include:

  • Bottom trays 
  • Cell packs
  • Pots
  • Tray lids

Alternate Seed-Starting Methods

Close-up of soil blocks with young sprouted seeds on a white windowsill. Soil blocks are compacted masses of soil, formed into cube shapes. The seedlings are young and consist of thin vertical stems and oval green leaves with slightly narrowed tips.
The soil block becomes the growing media and the “pot” for seedling development.

Soil blocking and winter sowing are two techniques that utilize fewer resources and materials. Still, they rely on a few to support healthy seedlings, and it’s helpful to have a quick way to sterilize your plant containers.

Soil blocking is a technique that uses a blocking tool and formulated soil mix to create blocks for seeding. The soil block becomes the growing media and the “pot” for seedling development. Soil blocking relies on fewer resources, eliminating the need for cell packs or small pots (and doing away with the need to wash them). Materials to sanitize include the blocking tool and holding trays that house the blocks.

Winter sowing is a resourceful method that requires only a few household supplies. It repurposes plastic containers, modified to become mini greenhouses. The containers provide insulation for seeds in the soil until they germinate under natural conditions outdoors. Materials to sanitize include the containers themselves. Wash them in warm, soapy water to prep for soil and seeds (they don’t require additional bleaching or alcohol solutions unless already used for growing).

Container examples:

  • Milk jugs and water bottles
  • Salad greens clamshells
  • Deli trays and platters
  • Large takeout containers

Initial Soap Bath

A yellow-gloved hand holding an orange sponge above a pink tub filled with soapy water, with suds visible.
Dish soap or detergent works well. 

The first step is to remove loose debris and remnants with a brush or cloth. Next is a bath in soapy water for pots, trays, and cell packs. Dish soap or detergent works well. 

Wash individually or place the supplies in a tub or bucket of soapy water and rinse each clean. Follow the soap bath with either bleach, alcohol, or other sanitizing solution, highlighted below.

Method One: Bleach Solution

A light blue basin being filled with water from a white bottle, with a green cleaning cloth placed beside it on the tiled floor.
Add one part household bleach to nine parts water in a large bucket or tub.

The first way to sterilize is to soak the plant containers in a diluted 10% bleach solution. It helps to have two large tubs or bins for this one. If you grow in bulk and have a lot of pots to disinfect, a small kiddie pool, trough, or pond liner is useful. 

Add one part household bleach to nine parts water in a large bucket or tub. Soak the supplies for at least 10 minutes and up to 20. Have a clean tub of water nearby to dip and rinse the soaked pots or rinse them under running water.

Wear gloves when working with the bleach solution, and protect skin, eyes, and clothing. Use the solution within two hours to preserve the concentration.

Method Two: Alcohol Spray

A hand holding a light blue and white spray bottle with a nozzle, ready to be used for cleaning purposes.
Wipe the equipment with the alcohol cloth or spray all surfaces with the solution.

As an alternative disinfectant to bleach, wiping or spraying with alcohol is an easy way to sterilize plant containers. You can do this as you work or for smaller batches of containers and trays.

Starting with clean, debris-free containers, use 70% undiluted isopropyl alcohol (rubbing alcohol) on a cloth or in a spray bottle. Wipe the equipment with the alcohol cloth or spray all surfaces with the solution. There’s no need to rinse with water after application.

Alcohol is also useful for disinfecting pruners and other tools at any time during use. A spray, dip, or wipe with the alcohol sanitizes tools against the spread of fungal or other disease problems as you move from plant to plant when pruning and clipping.

Removing Mineral Deposits

Hands holding a terracotta pot with white deposits, scrubbing it clean using a sponge.
Use a scrub brush or scouring pad to remove the deposits.

To get rid of that pesky, unhealthy, and unsightly buildup along the interior rim, do the pre-wipe with a rag or brush to remove any loose debris. Give a soap and water bath, followed by bleach solution dip if you use that method. Then, use a scrub brush or scouring pad to remove the deposits.

For clay and terracotta pots, do this inside and out. For stubborn buildup, scrape it off with steel wool, a wire brush, or a blade. Follow up with the alcohol rub or spray if preferable to the bleach.

Any garden pot benefits from this treatment. Salt and mineral deposits can cause stems to desiccate as they have contact with the residue or as they trail in the case of terracotta with deposits inside and out.

Dry Time and Disposal

A close-up of stacked terracotta pots with smooth edges and drainage holes, resting on small gravel.
Drying keeps any liquid bleach or alcohol from soil contact.

Let sterilized containers dry completely before using them for seeding or planting. Drying keeps any liquid bleach or alcohol from soil contact.

Use both the bleach and alcohol solution to clean any tools or greenhouse/growing surfaces. Remaining bleach and water can wash paved surfaces and mildewed areas, too. To dispose of the excess solution, remove it from the garden and dilute it with fresh water continually as it pours from its bin.

Other Treatment Solutions

A variety of cleaning products in plastic bottles with spray and screw tops, arranged in a group against a plain wall.
They eliminate fungal, viral, and bacterial pathogens.

There are a number of commercial products available to sterilize growing equipment. These may be good options if you do a lot of growing, bulk seeding, and potting. They offer bleach alternatives like hydrogen peroxide combination disinfectants (OxiDate and SaniDate are organic options, for example). 

seraaraQ-salt products (Green-Shield, Physan 20, KleenGrow) are quaternary ammonium chloride salts that disinfect greenhouse surfaces, supplies, and flooring. They eliminate fungal, viral, and bacterial pathogens, and some have plant applications during the growing process.

Share This Post
Close-up of a gardener cleaning a garden tool - a black spade under running water in a sunny garden.

Gardening Tips

A Beginner’s Guide to Cleaning and Disinfecting Your Garden Tools

Much like a chef has a favorite knife, every gardener has a favorite tool. The key to their longevity and effectiveness lies in how well they’re taken care of. Well-maintained and cleaned tools also limit disease spread in the garden, leading to healthier and happier plants. In this article, gardening expert and hori-hori aficionado Christina Conner shares some of her top tips for taking great care of your garden tools.

The open doors of a small glass greenhouse reveal organized shelving and growing plants.

Gardening Tips

11 Tips for Organizing Your Greenhouse

Does your greenhouse feel like a chaotic mess? Are you starting a new greenhouse from a blank slate? An organizational strategy can help you create the most efficient and beautiful indoor growing space possible. Former organic farmer and greenhouse grower Logan Hailey offers 11 incredible tips for planning and organizing your greenhouse.

Spring Garden With Seeds Being Winter Sown in Red Cups

Gardening Tips

11 Gardening Tasks to Prepare Your Garden for Spring

Spring is around the corner, and your vision for a beautiful spring garden is at your fingertips. But what can you do to help ensure your spring garden is a success? In this article, certified master gardener Liz Jaros shares her top tips to prepare your garden for successful spring plantings.

container gardening mistakes

Gardening Tips

17 Vegetable Container Gardening Mistakes to Avoid

Are you creating a container garden for your vegetables this season? Don't fall victim to some of the most common mistakes you can make when vegetable gardening in containers. In this article, gardening expert and former organic farmer Sarah Hyde walks through the most common mistakes container gardeners make with their vegetables.