Why Are My Chili Pepper Seedlings Dying? (Resolved!)

Over recent years, chili peppers have grown in popularity both here in the US and across many other parts of the world.  Dedicated growers have made strains that have increasing levels of heat.  There are a number of different ways chili peppers can be preserved for use throughout the year, making them an ideal crop for the homesteader.

There can be a number of reasons chili pepper seedlings are dying unexpectedly, and these include;

  • Over or underwatering
  • Fungus, bacteria, or virus
  • Poor quality potting soil
  • Stem damage
  • Transplant shock

Over Or Underwatering

Chili pepper seedlings, like all plants, need water to grow.  The problem comes when they receive too much or too little water.  Typically, chili pepper seedlings are overwatered rather than underwatered and this can lead to waterlogging of the soil.

Chili pepper seedlings’ roots need access to air as much as they need access to water.  When their potting soil is waterlogged, the roots don’t have enough access to air and the seedlings can rapidly die off.

As a general rule, chili pepper seedlings should be watered little and often, rather than drenching the soil and leaving the seedlings in soggy soil.

I prefer to place my whole seed tray in a larger tray of water, give it a minute or two to absorb some of that water, then move the seed tray to a dry location so the excess water can drain away.  I have had great success using this watering method.

Underwatering can be just as harmful as overwatering.  If the chili pepper seedlings are allowed to completely dry out, they will wilt.  When plants wilt, their internal cells can be permanently damaged and the seedlings may never recover.

Fungus, Bacteria, Or Virus

There are a surprisingly large number of fungi, bacteria, and viruses looking to take advantage of and ultimately kill chili pepper seedlings.  Working out which one is affecting your chili pepper seedlings may allow you to save your seedlings before they die or prevent the same thing from attacking future batches of seedlings.  

Some of the most common diseases are detailed below.

Damping Off

Damping off is a generic term used to describe a number of different soil-borne fungi that can quickly kill chili pepper seedlings.  The fungi spring into life when exposed to warm, damp conditions.

It is usually only very young seedlings that are killed as a result of damping off, older, stronger seedlings are usually able to shrug off the bacteria with few ill effects.

Damping off is normally fairly easy to identify.  The chili pepper seedlings will usually all collapse in a short space of time and may turn to mush.  

There is currently no known cure for damping off and prevention through good hygiene practices is the best way to stop your chili pepper seedlings from dying as a result of damping off

Growing your chili pepper seedlings in old potting compost, or worse, garden soil is the most likely way to kill your chili pepper seedlings through damping off.

Seedling dying as a result of damping off

Fusarium Fungus

Fusarium Fungus is a soil-bourn pathogen that can remain in the soil for an almost indefinite length of time.  The fungus attacks almost every species of plant it comes into contact with and it can run rampant through a greenhouse or polytunnel.

Prevention is better than cure with Fusarium Fungus. Employing strict crop rotation, never reusing old potting compost, and thoroughly cleaning all pots and trays before use will help reduce the chances of the fungus being present.

The first sign a chili pepper seedling has Fusarium Fungus may be that the seedlings begin to wilt.  This can cause the grower to overwater to try to reduce the wilting.  Further symptoms of Fusarium Fungus include stunted growth and yellowing of the leaves.  Ultimately the seedling will succumb to the fungus and will die.

There are currently a limited number of treatments on the market for Fusarium Fungus and all the ones I know of are only licensed for professional use only.

Any seedlings infect with Fusarium fungus should be disposed of (including their potting compost and seed tray) either through burning or with the general household waste.  Infected seedlings should never be disposed of in the compost heap.

Tobacco Mosaic Virus

Tobacco Mosaic Virus, which is often referred to simply as TMV, is named after the first plants the virus was discovered in which were Tobacco plants.  TMV affects a number of different plants, but chili pepper and tomato seedlings seem to be especially vulnerable.

Symptoms of Tobacco Mosaic Virus include curling of the leaves, stunted growth, and yellowing of the whole plant.

The most common way TMV is spread between plants is thanks to human interaction.  If we touch one plant that is infected with TMV, we can actually spread it to other plants we touch.  According to the Pennsylvania State University

Tobacco products, particularly those containing air-cured tobacco, may carry TMV. Flue-cured tobacco, used in making cigarettes, is heated repeatedly during its processing, thereby inactivating most if not all TMV. When tobacco products are handled or kept in pockets, hands and clothing can become contaminated with TMV and be a source of the virus. TMV is not spread in the smoke of burning tobacco.

There is currently no known cure for TMV and infected plants should be either burnt or disposed of with the household waste.

Prevention is the only way to control TMV and basic practices like washing hands thoroughly before handling seedlings will go a long way to preventing the virus from infecting your plants.

Poor Quality Potting Soil

Developing chili pepper seedlings require the right level of nutrients to be able to develop properly. When poor quality potting compost is used there may not be enough nutrients available for the developing chili pepper seedlings.  The same is true when old potting compost is reused or garden soil is used.

To give chili pepper seedlings the best chance of growing into strong, healthy plants, always use new, specialist seed compost from your local supplier.  Recently I have had good success using seed starter compost purchased from Amazon.

Stem Damage

Stems damaged when the seedlings are transplanted to new pots is another major killer of chili pepper seedlings.  Chili pepper seedlings have very delicate stems. They are easily damaged if roughly handled during transplantation.

I have found the ideal way to transplant chili pepper seedlings is by holding the leaves between my finger and thumb, then using a pencil to gently lift the seedlings out of the soil.  I then use the pencil to support the seedling whilst moving them to their new pots.

Once a chili pepper seedling’s stem has been crushed, the result is usually that the seedling dies fairly quickly.

Transplant Shock

Transplant shock of chili pepper seedlings is probably one of the least well-known reasons chili pepper seedlings die.  As the name suggests, the seedlings appear to go into shock as a result of being transplanted from the original seed tray to a new pot.

There are no real symptoms of transplant shock other than the fact the seedlings simply collapse and die shortly after being transplanted.  Both chili pepper and tomato seedlings seem to be especially vulnerable to transplant shock.

To reduce the chances of chili peppers dying from transplant shock, try to make sure the old and new compost are roughly the same temperatures, work quickly when transplanting the seedlings, and never transplant the seedlings during the hottest part of the day.

Arya Patel

Arya Patel is HomesteadSavvy.com’s fruit and vegetable editor. Arya has been homesteading for well over a decade and over that time she has grown countless varieties of fruits and vegetables. She aims to become completely self-sufficient over the next 5 years.
Fruit & Vegetable Editor