Why Are My Tomato Seedlings Dying? (Explained)

Tomatoes are the ubiquitous plant of any self-respecting homesteader.  Tomatoes can be eaten raw, cooked, and most importantly, preserved in a number of different ways.  Anyone wanting to become even remotely self-sufficient will want to master growing tomatoes.

I grew my first tomato plants over 30 years ago, and I still love that smell of tomato plants when I walk into my polytunnel.  If there is one question I get asked more than any other about growing tomatoes, it is ‘why did my tomato seedlings die?’

There are a number of different reasons tomato seedlings die before they have had a chance to grow into decent-sized plants.  These reasons include;

  • Under or overwatering
  • Exposure to cold weather
  • Fungus, bacteria, or virus
  • Transplant shock
  • Stem damage
  • Poor quality potting soil

Overwatering Or Underwatering Tomato Seedlings

We all know plants need water to grow, but most don’t need anywhere near as much as we give them.  One of the classic errors made by people growing tomato seedlings is giving them too much or too little water.  

When we give tomato seedlings too much water, the soil becomes waterlogged. 

Tomato plant roots need access to oxygen as much as they do water.

When the potting soil is waterlogged the air is forced out of the soil completely.  The tomato plant’s roots effectively can’t breathe and the plant dies.  

One common way tomato seedlings become waterlogged is when they are grown in pots or trays that don’t have sufficient drainage holes.  It is very important that water is allowed to escape through the bottom of the pot or tray otherwise the potting soil will quickly become waterlogged.

If the tomato seedlings are given too little water, the cells that make up the plant begin to decay and dry up and the plant will no longer be able to hold itself upright.  The leaves of tomato plants that have been underwatered will start to curl and become dry.  

Tomato seedlings can dry out very quickly, especially when grown in a warmer greenhouse or polytunnel.

Exposure To Cold Weather

Tomato seedlings are not hardy at all.  They will quickly be killed off if they are exposed to temperatures below 50°F (10°C).  Even tomato seedlings being grown undercover in a greenhouse or polytunnel can be chilled if the temperature falls low enough.

I like to have a small roll of horticultural fleece in the greenhouse.  That way, if the weatherman suggests the temperature is going to drop, I can cover my tomato seedlings with fleece, which should keep the temperature up enough to get my tomato seedlings through.

Alternatively, you can use a greenhouse or space heater to add warmth if it gets too cold. 

Fungus, Bacteria, And Viruses

Unfortunately, there is a wide selection of different fungi, bacteria, and viruses that will take advantage of young tomato seedlings.  Knowing which has made your tomato seedlings sick and start to dye off is the first step to treating the problem and hopefully saving the rest of your seedlings.


Damping-off is probably the most common cause of tomato seedlings dying.  Damping-off is a general term used to describe seedlings that suddenly die off as a result of a number of different soil-bourn fungi.  The fungus is stimulated into growth itself by the warm, moist soil the seedlings are living in.

Normally, seedlings are killed by damping off soon after emerging from the soil.  Older, more mature seedlings can often shrug the fungus off and grow without being affected.  

Damping-off is usually easy to identify.  The tomato seedlings suddenly seem to collapse and turn to brown or black mush.

There is currently no known cure for damping off.  Instead, it is better to try to prevent damping off in the first place by making sure all seed trays and potting equipment are kept clean before and during use.

Using fresh potting compost for your tomato seedlings will also reduce the chances of damping off.  Reusing old compost or garden soil increases the chances of tomato seedlings damping off.

Seedling dying as a result of damping off

Fusarium Fungus

Fusarium Fungus is a pathogen that attacks the seedlings of almost any plants it comes into contact with. It can stay alive in the soil for an almost indefinite amount of time, lying in wait for seedlings to emerge.

Fusarium Fungus can run rampant through a greenhouse or polytunnel and getting it under control is of the utmost importance.

The first sign a tomato seedling is suffering from Fusarium Fungus is the seedling wilting, much like when it is underwatered.  This first symptom can often lead to people overwatering the seedlings as they try to compensate.  Further symptoms include yellowing of the leaves and stunted growth.  Eventually, the seedling will succumb to the fungus and die.

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.  

Any seedling of plants that have Fusarium Fungus should be disposed of (not in the compost heap).

There are treatments on the market to tackle Fusarium Fungus, but the vast majority are licensed only for use by professional contractors.

Early Blight Alternaria

Early Blight Alternaria is prevalent in areas where the air is naturally warm and humid and can be especially problematic in warm and humid greenhouses and polytunnels.

Typical symptoms of Early Blight Alternaria are the lower leaves of the seedlings turning yellow or spots developing on the lower leaves.  Early Blight Alternaria can ultimately cause damage to the leaves, stem, and fruit.

As with so many fungi that attack tomato plants, prevention is better than cure.  Allowing sufficient space between plants to increase airflow will reduce the chances of Early Blight Alternia taking hold, as will watering only the soil, and not the plant.  Taking care to keep the leaves and stems dry is probably the most important aspect to remember when watering tomato seedlings.

There are a couple of spray treatments available, but they tend to only slow the progress of the fungus rather than eliminate it.

As with other tomato plant problems, practicing good crop rotation, never reusing old potting soil, and cleaning pots and trays between batches of seeds is sound advice.

Tobacco Mosaic Virus

Tobacco Mosaic Virus (which is often referred to simply as TMV) is named after the first plant it was discovered in, which was the Tobacco Plant.  TMV affects many different plants but tomatoes and peppers seem especially susceptible to it. 

Symptoms of TMV include mottling and/or blisters on the leaves, as well as the leaves themselves curling.

TMV is a virus and rather than producing spores, it has to physically enter the plant via a wound or a damaged area of the plant.  Unlike many other viruses and bacteria, TMV doesn’t usually kill the host plant, but it does normally stunt its growth and cause long-term damage to the leaves, flowers, and fruit.

Tobacco Mosaic Virus has been known to survive and remain viable in dried plant material which had been dry for around 50 years!

There are currently no known treatments for TMV and any infected plants should be removed and burnt. TMV can be largely prevented through good garden hygiene and not reusing old potting soil.   

Transplant Shock

Transplant shock is the sudden collapse and death of a seedling after it is moved to a new location.  Transplant shock is mainly caused due to a sudden change in temperatures, both in the compost and surrounding air.  

Unfortunately, tomato and chili seedlings are especially prone to transplant shock.  To reduce the chances of seedlings becoming affected by transplant shock, make sure the new compost is kept in the same area as the seedlings so the temperature can equalize.  Make sure the seedling are watered well prior to transplanting and ensure the new compost is moist, but not saturated.  

When transplanting the seedlings work quickly but carefully and ensure you water them in well once they are all planted in their new home.  Also, always plant tomato seedlings deeper than they were in their old pot or tray.  Tomato seedlings actually grow better when planted deep and will grow roots from any section of the stem which is buried in the compost.  

Stem Damage

Tomato seedlings are easily damaged if handled incorrectly.  This is a problem for someone like me.  I don’t exactly have a delicate touch!  The stems of tomato seedlings are easily crushed when pricked out between finger and thumb.  

When transplanting the seedlings from their tray to the new pot, it is important to handle them by their leaves.  I like to use a pencil when transplanting tomato seedlings.  I hold the seedlings by their leaves and use the end of a pencil to ease it out of the compost.

A crushed stem almost always proves fatal to a tomato seedling.

Poor Quality Potting Soil

When seedlings are developing they require access to nutrients in the right blend.  Poor quality potting soil, or worse, garden soil, won’t have enough nutrients to support the seedlings’ development.  This lack of nutrients will lead to pale, spindle tomato seedlings that will fail to reach their full potential.

Always use fresh, specialist seed compost as it will have been developed to deliver just enough nutrients to the seedlings so they develop properly.

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