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12 Tomato Seedling Problems and Their Solutions

Planting tomato seeds in a perfect environment and still having issues with proper care is a big disappointment for all of us. Various tomato seedling problems may occur along the growth process.

As I write this, I have had a similar kind of experience. Going through these different stages of my unhealthy tomato seedlings, I have personally encountered various tips of dos and don’ts.

Like parents care a lot about their babies, it’s a mutual feeling for all the gardeners about their plants. Nevertheless, I am sure you are one of those plant fanatics like me floating in obsession.

There can be various tomato seedling problems such as:

  1. Droopy and Wilting Tomato Seedlings
  2. Purple Tomato Seedlings
  3. Slow Growing Tomato Seedlings
  4. White patches on your tomato Seedlings
  5. Brown leaves or spots on your Tomato seedlings
  6. Yellow leaves on your Tomato seedlings
  7. Leggy Tomato Seedlings
  8. Wavy and Brittle Seedling Leaves
  9. Black Fungus and Yellow Spots in Seedling Leaves
  10. Viral Problems in Tomato Seedlings
  11. Fungal Disease Problems
  12. Rushing to hardening the Seedlings

The right knowledge and proper care are always needed while you are embedding tomato seedlings.

The exhilaration starts from the initial budding of the stem. Inspecting their growth process every day is where our fascination hits in.

Generally, tomato plants show disease problems later in life. Sudden alertness strikes us when we see unusual signs in our plants. It is more alarming when prominence appears at the early seedling phase. A lot of questions might run through your head on “What’s wrong with my seedlings?”

An early detected problem during the seedling phase gives an extra mile to recover soon. To cater to these doubts of problems, let us go through the possible causes and solutions.

1) Droopy and Wilting Tomato Seedlings


One of the reasons behind droopy and wilting seedlings could be overwatering or underwatering of the plants.

Though watering your plants do not take much effort, correct know-how of when and how to water is essential.

Overwatering creates a pool with drowning seedlings.

Hence, the compact drenched soil with too much moisture makes the plant difficult to breathe.

Underwatering, on the other hand, makes the seedlings fragile.

This is because the soil is arid, which causes dehydration. Hence, it hinders the transportation of enough nutrients to the entire plant.

It is one of the major concerns for many people on how often to water your tomato plants. Let us look into it.

Droopy downward facing leaves


It would be best if you have a consistent watering schedule for the healthy growth of your seedlings.

Rather than going for random guesses on how often to water, watering your tomato seedlings once a day is good.

Water them consistently, and most importantly, do it correctly on how much?

How much to water your tomato seedlings?

When you pour water, be careful not to flood the soil but keeping it moist. The dampness should reach around 6-8 inches under the ground. This stimulates the growth of the plant.

2) Purple Tomato Seedling Problem


As we know, healthy plants are mostly rich green in color.

Likewise, we might come across other color variations such as Purple or reddish leaves in tomato seedlings. This is not a good sign!

One of my friends’ tomato plants had a similar issue during its seedling phase, with the stems turning purplish. It literally stalled down the growth of the plant.

You do not need to worry much. It is basically a sign of nutrient deficiency.


Induce proper nutrients to the seedlings to help them revive.

While transplanting, you can add some fertilizers and bone meals too. They are rich in phosphorus which helps your seedlings to grow healthier.

3) Slow Growing Tomato Seedlings


You might be taking well care of your tomato seedlings with the best light settings and soil conditions. Yet, they are growing at a pace of a snail. Of course! This is not natural.

Here, the soil is not warm enough to accelerate its growth.


Maintaining soil temperature is equally important as having other rudiments fulfilled.

The temperature needs to be sufficiently warm to bloom the buddings faster.

So get your soil temperature right while planting the seeds and maintain it well with around 18 degrees Celsius heat.

Initially, during the germination process, it is best to have 21 to 26 degrees Celsius temperature. It will cool down once it sprouts.


Mist sprays are usually sprayed with normal temperature water. However, it would be best if you go with warm mist sprays for warming your plant soil.

You can also use heat mats underneath the seed trays. It should be kept in warmer sites.

On the verge of bettering your seedlings, sometimes you might go back to square one if not done properly. Hence, be cautious about the adverse effect of too much heating also.

Read the article ” 12 Ways to Speed Up Tomato Growth ” for more information.

4) White Patches on Your Tomato Seedlings


You might be having some white patches/spots or coated white substances on your tomato seedling leaves. This is usually caused due to Sunscald OR bacterial diseases.

Sunscald is triggered by excessive exposure to sunlight whereas Fungal or bacterial diseases may prevail with congestion and overwatering.


To eradicate the whiteness in the leaves, you need to be wary about good soil drainage and proper air circulation inside the soil. Ensure that the seed and the area for planting are well sterile.

If already damaged, eliminate the infected part of the plant and then re-pot it to a sterile condition.

Seedlings need an adequate amount of sunlight. During the initial phase of hardening the seedling, please place it in the direct sun for few hours every day.

High exposure of your seedlings in the scorching outside sun creates sunscald.

One of the solutions for this unavoidable situation is using plant sunscreen.

5) Brown leaves or spots on your Tomato seedlings


This is another similar issue to the white patches.

The brownness can cause due to extreme overwatering or underwatering. It is also a sign of bacterial, fungal, or soil-borne diseases.

Scrunchy Brown Leaves


The worst part is that there is the least chance of revival once the whole stem turns brown in color. However, if it has only affected the leaves, try to remove them immediately.

Maintaining a sterile well drainage basket with good air movement is always recommended to avoid infestations.

6) Yellow leaves on your Tomato seedlings


Your seedling could be suffering from malnourishment which is leading to yellow leaves. Low Nutrients and underwatering are the foremost reasons behind this problem.

Yellow tinted leaves


Supply enough nutrients to your little seedlings. The food wastes from our kitchen, forming a great source of organics, contribute as nutrients for the baby seedlings to nourish.

To be precise, rotted organic matter and waste composts will help the babies become tougher.

You can obtain the rotted organics through tea composts, banana peels, or potato skins. It is a natural method that most plant owners use at home.

Water adequately in a consistent manner with a good drainage system. Similarly, you can also spray the leaves of the seedling with diluted liquid fertilizers.

In my opinion, applying organic and natural composts from the start helps a lot.

7) Leggy Tomato Seedling Problems


It is fascinating to see plants/ seedlings slant towards the direction of sunlight.

I encountered a similar circumstance with my indoor succulents. I had kept them near the window in a small room. It was astonishing to look at those cuties tilt towards the sun.

This might seem normal for many of us, but tilting towards the sun is actually the consequence of our poor lighting system. The stems become long and lanky, generating small leaves.


To provide enough lighting, make sure you provide 12 – 16 hours of artificial lighting or 6 – 8 hours of natural sunlight.

  • For natural lighting:

It is always better to place your seedlings near the sunny window or outside in direct sunlight exposure. A favorable temperature is above 10 degrees Celsius.

Personally, I have always loved opting for natural methods like sunlight exposure.

An artificial lighting system is also an option when the weather is not in our favor. Many of my friends and I have used it with our plants. As a result, the effect was prominent.

  • For artificial lighting:

The best ones for the lighting system are fluorescent or LED lights. They can be placed around 4 inches above the plants and raise gradually as the plant grows.

These lights deliver a good light spectrum and low heat output leading to the proper growth of the plant.

8) Wavy and Brittle Seedling Leaves


The dehydration of the plant determines the changing shape of the leaves.

The tomato plant starts to curl its leaves after a day without any water. Curling happens to preserve its moisture.

Too much artificial or natural lighting dries out the plant fast.


The right amount of watering is necessary to avoid dryness. Yet, do not overflow the soil but keep it damp.

You can also use natural minerals containing a mix of vermiculite or perlite.

9) Black Fungus and Yellow Spots in Seedling Leaves


Vermins easily attack weak seedlings. The common ones in the indoor gardens are Whiteflies. They leave behind yellow spots after pulling out the latex from the seedlings.

These Whiteflies suck more than they can digest, which leads to the defecation of honeydew on leaves. They are sugar-rich sticky liquids. Henceforth, the black fungus nurtures upon the honeydew creating its existence.

Yellow Spots on the leaves


You can use sticky traps around your seedlings that seize the insects and flies hovering around. Therefore, it creates a shield before the damage is done.

Another alternative could be using insect-killing soaps like Safer Brand. It eradicates the whitefly plagues and is suitable to use once the seedlings grow larger to plants.

10) Viral Tomato Seedling Problems


Various viruses can infect your tomato seedling. The transmission can happen from human touch or insects. Some of the viruses are:

Cucumber Mosaic Virus (CMV): CMV causes a tomato seedling to become shaggy, yellow, and undersized from its normal growth.

Getting infected during the seedling stage of the tomato plant leads to a stoppage in growth. There is extreme leaf distortion like rolling or cupping up the leaves.

Tobacco Mosaic Virus (TMV): This virus is usually common in tomato plants. They are very infectious and easily transmitted.

The symptoms get prominent with cuts and dappling of the leaves with a papery texture. It usually spreads through our/ gardeners’ hands to plants. Tobacco pathogens cause the virus.

Curly Top: As the name defines itself, the leaves curl with deformities. Alongside, the purple leaf veins also appear. As similar to other viruses, their growth also gets stunted.

Moreover, your seedlings might have fewer chances of survival if they are attacked with curly tops. This is so because the plant is at a very earlier stage.

Thrips: Thrips are insects that might attack your seedlings. It leaves the seedlings with speckled grazes, followed by purpling of their leaves at the edges.


As we know, viruses breed in dirty areas.

The best way to avoid all these diseases is to maintain good sanitation.

It is best if you are careful while handling the plants and the tools you are using. Removing the weeds time and again also helps a lot. Other precautions or solutions would be to control insect infestations.

11) Fungal Disease Problems


If you face Fungal problems, then trust me, it is the most common issue in Tomato seedlings. I have had it in mine too.

As I have known, they crawl up even with our finest gardening care. Some of them are:

  • Botrytis: It is dangerous once it gets into the stem and kills the whole plant. You will see patches of black decays.
  • Damping: Tomato seedlings start to droop, get yellow and then die off when they are damp. Likewise, they become energetic in wet and cool areas.
  • Early Blight: You will experience this disease on your tomato seedlings, mostly in warm temperatures with high humidity. It stops the growth and ultimately attacks the whole plant, for instance.


You can apply copper fungicides for fungal problems.

Since one of the crucial reasons behind fungus accumulation is overwatering, strictly avoid it. Besides, cleaning off the debris and regulating humidity is equally important.

12) Rushing to Hardening the Seedlings


When you are in a big rush to grow your baby tomato seeds, it might backfire.

Sudden exposure to the outside environment in the roasting sun will stress out the seedlings.

Seedlings take time for their environmental adaptation to nurture themselves.

Gradual adjustment to the outdoor environment                                (Source:


Slowly try to adjust the indoor tomato seedling to the outdoor environment in the sun.

You can perform it by taking the plant outdoor for some hours and again bringing it in. Please do it for a week, and that is how the seedling will adapt to your garden space.

In hindsight, you can also find out whether your tomato plants are healthy or not. Click Here to explore more in detail.

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