It’s fun to grow tomato plants in a garden or a┬ácontainer. But when you start growing seedlings, there may be a problem that some of them are dying. I wanted to know what could be the reason for this and have written my research below.

Your tomato seedlings are dying because of overwatering or underwatering. Too much water will cause rotting while too little water will dry out the plant. The tomato seedlings may get infected by fungal disease that will kill them when there’s too much moisture in the soil.

I’ve written a lot more details about these factors and some more that you may find useful when figuring out the problems with your own tomato seedlings dying.

1. Underwatering or overwatering

One of the most common problems faced by seedlings is a lack of water. And this could happen with underwatering or overwatering.


You will notice that the leaves are turning yellow, dry, and drooping due to underwatering. And they will be turning yellow, wilting, and developing blisters if the problem is overwatering.


We sometimes miss the watering schedule causing the soil to dry out. Keep doing this for long and your seedlings will die. The other danger is from overwatering where we want to be too careful and keep adding water to the soil.

The overwatering causing the seedlings roots to rot. This means the roots cannot supply the nutrients and moisture to the seedling causing it to die.


My suggestion is to keep a daily schedule of checking on your tomato seedlings. You need to check whether there’s sufficient moisture in the soil.

You can do this using a moisture meter but I have a simple method for you. Just stick your finger 1-2 inches into the soil and check the moisture. If the tip of your finger does not feel moist, you need to water the soil.

If your seedlings are underwatered, you will need to water the soil deeply so the soil can get back it’s texture and the moisture can reach the roots.

If your seedlings are having root rot, you may need to dig up the soil and cut off the damaged roots. If most of the roots are damaged, you’ll need to plant a new seedling.

2. Poor soil

Another common problem when growing tomato seedlings is using poor soil. This can happen whether you’re starting seeds indoors or directly planting seedlings outdoors.


If you use poor soil, the tomato seedlings might not even germinate. Even if they do germinate, their growth will be stunted. And in the worst case, the seedlings will wilt and eventually die.


Whether you use potting soil or garden soil, it has to have the right texture and nutrients for the tomato seedlings to grow well. It also needs to be free from pests, diseases, and chemicals.

Tomato seedlings like the soil texture to be loose enough so moisture and nutrient circulation is good. But it does not like the soil to be soggy when watered.


If you’re growing the seedlings in pots, it’s best to use potting soil rather than garden soil that could have the problem of bad texture, lack of nutrients, or the other problems I mentioned.

If you’re growing the seedlings outdoors, make sure to have a soil test done to check whether the garden soil is appropriate. If not, you will need to either amend the soil, build a raised-bed garden with the right soil, or grow in containers.

3. Lack of light

Tomatoes are a warm-season plant that needs full sunlight to grow their best. This means you need to give the seedlings at least 6-8 hours of direct sunlight every day.


If the tomato seedlings don’t get the required sunlight, their growth will be stunted. They will become legging as the seedlings try to reach out and find the required sunlight. The leggy seedlings will eventually fall over as the plant can’t hold it’s weight and eventually die.


If you’re growing tomato seedlings indoors, the main reason for lack of light will be that the sunlight is not reaching them. If you’re using indoor lights, the intensity might not be what is required by the seedlings.

If you’re growing them outdoors, the seedlings may be getting shade due to obstructions like a wall or a larger plant.


If you’re planting the seedlings outdoors, this may not be a problem as long as you pick the right location that gets full sunlight. But if you’re growing the seedlings indoors, you need to place the seedling tray near a window that gets good sunlight.

The other option you have is to use the right indoor lights with the required intensity for growing the tomato seedlings.

Make sure the seedlings are getting light on all sides of the plant otherwise they will bend on one side. You can turn the seedling tray every day to do this.

4. Lack of warmth

You know a tomato is a warm-season plant which means it grows best in temperatures between 75-85 degrees. If the temperature drops below 50 degrees, the seedlings will be in trouble.


If you’re growing indoors and the temperature drops a little, it will stunt the growth of the seedling.

But if you’re growing the seedlings outdoors and the temperature drops below 50 degrees for many days or nights, the seedlings will die due to the cold.


The main reason for a lack of warmth is if you’re not giving the seedlings the right heat. If you’re growing the seedlings indoors, you may not be keeping a check on the temperature.

If you’re growing the seedlings outdoors, you may have started before the last frost date of your area. Or you may not be taking care of the seedlings when the night temperature occasionally drops.


If growing indoors, I would suggest using a heat mat to keep the right temperature.

If you’re growing seedlings outdoors, make sure to do so only a few weeks after the last frost date of your area. If you find that the night temperatures are dropping, you will need to cover the tomato seedlings with a plastic bag or bucket at night.

If you’re growing the seedlings in a container, you can just move the container indoors for the night when the temperature is going to drop.

5. Transplant shock

Whether you grow tomato seedlings indoors or buy them from a local garden center, you’ll need to transplant them either in a bigger container or outdoors.

If the seedlings are transplanted without proper care, they will suffer from transplant shock.


When the seedlings are affected by transplant shock, they come under stress. This will cause the seedlings to not grow properly. They won’t be able to absorb the required nutrients, moisture, and sunlight.

The seedlings will suffer from a lack of nutrition and eventually die.


Hardening is a process where you gradually make the seedlings acclimatized to the outdoor environment before the transplant. The main reason for transplant shock is you don’t give the seedlings the right amount of hardening.


The solution is to harden the seedlings well before you are ready for the transplant outdoors or in a container.

You can keep the seedlings outdoors for 1-2 days for 3-4 hours but not in direct sunlight. Make sure there is no heavy rain or wind when you will do this.

For the next 2-4 days, you can keep the seedlings outdoors for 5-6 hours and give them some direct sunlight to get used to.

For the next 5-6 days, you can keep the seedlings outdoors for the full 6-8 hours giving them exposure to the direct sunlight.

After this period, the seedlings will have hardened well to the outside environment and will be ready for the transplant.

6. Root damage

Roots are probably the most crucial part of your tomato seedlings. Damage to roots means a high risk of your seedlings dying.


If the roots are damaged to a large extent, they will not be able to provide nutrients to the seedlings and they will die.


There can be many causes of root damage including overwatering causing root rot, pests, and diseases attacking the roots, or damage to the roots when transplanting from a tray to a pot or garden.


You need to take care of the roots of the seedlings by regularly checking for signs of problems. We have seen how to solve the issue of overwatering. And I’ll give more details on how to fix pest and disease issues that affect the roots.

When transplanting the seedlings from a tray, make sure to handle the roots with care. You should always hold the stem of the seedlings and avoid touching the roots as much as possible.

Place the roots completely in the soil and make sure to cover some parts of the stem along with the roots to grow even stronger roots from the stem.

7. Fertilizer burn

Tomatoes are a hungry plant that needs to be fertilized. But you need to be careful not to apply too much of it as it can cause fertilizer burn.


If your tomato seedlings are suffering from fertilizer burn, the leaves will wilt and turn yellow or brown. The roots are getting damaged and they won’t be able to supply the nutrients to the seedlings.


The main cause of fertilizer burn is if you are adding a lot of nitrogen-rich fertilizer to the soil when growing the seedlings. You need to provide the right amount of fertilizer based on the type and instructions by the manufacturer.


I suggest adding a slow-release fertilizer only when the true leaves of the seedlings have appeared. True leaves are the second set of leaves that grow on the seedling. Make sure to use only the amount as specified by the manufacturer.

The slow-release fertilizer will be available to the roots when you water the plant. As it’s slow-release, the fertilizer will be available for a few weeks before you need to add it again.

You can also use a liquid-fertilizer instead to spray it on the soil and the seedlings for immediate effect. But make sure to dilute it well before using it.

8. Lack of nutrients

Tomato seedlings need a lot of nutrients to grow well. Once the seedlings have germinated, you will need to provide additional nutrients to them.


If the tomato seedlings don’t get the right nutrients, their growth will be stunted. The leaves will turn yellow and fall off if the lack of nutrition continues. There’s a high chance of pests and diseases attacking the plant. And eventually, the seedling may die.


The main cause of the lack of nutrients is not providing the right fertilizer to the seedling when it’s in the growing stage.

The other issue may be that you are providing fertilizer to the seedling but the amount is not sufficient as per the instructions. If you have bad soil, the nutrients from the fertilizer may wash away too quickly and not be available to the roots.


You need to keep a schedule where you provide either a slow-release or liquid fertilizer to the tomato seedlings. You can add the slow-release fertilizer 2-4 times during the growing season. Usually, adding this fertilizer every month would be beneficial. But it’s best to follow the instructions of the manufacturer.

You can also use liquid fertilizer instead but that has to be added every two weeks in the right amounts. You could even dilute the liquid fertilizer a lot and use it for watering the plants every day.

9. Diseases

There can be several different types of diseases like fungal, bacterial, and viral that could infect the tomato seedlings.

Some of the fungal diseases include damping, early blight, and fusarium wilt. Some of the bacterial diseases include leaf spot and bacterial canker. And some of the viral infections could be tobacco mosaic virus, spotted wilt, and curly top.


Some of the diseases will just cause cosmetic problems like white, brown spots on the leaves. But some of the diseases are fatal to the tomato seedlings. They will cause the leaves and stem of the seedling to change color and texture but also end up killing the plant.


Fungal diseases are caused because a moist environment has been created that attracts fungal infections. Such disease could also be carried by pests and insects. They can also reach the seedling when soil is splashed on the foliage.

Bacterial and viral diseases can reach your tomato seedlings when carried over by insects. The insects can infect the seedling through a wound in the plant, by eating into the plant, or just through the pores in the leaves.


You can prevent fungal infections by avoiding a moist environment for the seedlings. Use a watering can, drip-irrigation, or soaker hose to water them. Avoid using sprinklers or sprays that will splash water all over the foliage.

watering can
Watering can at the HortiPro Exhibition

You can water the seedlings in the morning so that the excess water can evaporate once the sun comes out. You can also wipe the excess water from the foliage with a clean cloth.

Make sure to allow plenty of air circulation among the plants in your garden including the seedlings.

Once the seedling is infected by a fungal disease, you can cut off the infected part. The remaining part should continue to grow without problems. But if the infection is on the entire plant, there’s not much to save the seedling.

Bacterial and viral diseases are hard if not impossible to treat once they have infected the plant. The best way to protect your tomato seedlings is with prevention.

If possible, try to get a tomato seedling variety that is resistant to some of the bacterial and viral infections.

10. Pests

white flies on pepper plant leaves
Whiteflies on my pepper plant leaves

There are several types of pests that can attack your tomato seedlings and cause problems for them. These pests could include insects and animals. Some of the insects include aphids, flea beetles, hornworms, whiteflies, cutworms, thrips, and fungus gnats. Some of the animals include rodents, rabbits, and deer.


Some of the pests like aphids will suck the sap out of the tomato seedlings. This will cause a lack of nutrients in the plant and it will eventually die if the infestation is large.

Ants farming aphids on my pepper plants
Ants farming aphids on my pepper plants

Some of the pests like cutworms attack the base of the seedling under the soil. They will cut off the supply of nutrients from the roots to the seedling and so the plant will eventually die.

Some of the pests may not directly harm the plant but they are carriers of bacterial and viral diseases that will infect your tomato seedlings and damage them.


The main reason pests will be attracted to the tomato seedlings if they are in a vulnerable spot. If the tomato seedlings are under stress or unhealthy, the pests find them an easy target.

The other reason for pests to reach your tomato seedlings would be a lack of beneficial insects that would attack and prey on such pests.


The best solution is to grow the seedlings indoors till they are a certain height. This can ensure the seedlings are healthy once you transplant them outdoors. They will be a lot less vulnerable to pests.

I would also recommend attracting beneficial insects like ladybirds and lacewings to the garden that can take care of some of these pests. You may consider using companion planting to grow some herbs or plants like garlic, onions together with the tomato seedlings. These plants can help repel some of the pests.

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