What’s Wrong With My Tomato Seedlings? 11 Pro Solutions to Common Problems

Seed starting is a time of auspicious excitement, but the good energy can quickly dwindle when you notice your favorite crops failing to thrive early on. Tomato seedlings are particularly prone to a range of problems, and figuring out what’s wrong with them isn’t always easy. 

These fast-growing crops can be overcrowded, underfertilized, overwatered, or need more sunlight, among a range of other similar-appearing issues. Symptoms often overlap, making pinpointing the issue even more challenging.

Let’s dig into this quick guide to diagnosing what’s wrong with your tomato seedlings and how to fix them.

What’s Wrong With My Tomato Seedlings?

Tomatoes are resilient garden crops that can bounce back from almost anything. If you notice any of these symptoms that something is wrong with your young sprouts, rest assured that you can likely save them without permanent damage. In the worst-case scenario, you can always sow more seeds and learn from your mistakes for next time.

Here are the most common problems with these seedlings and how to fix them.

Leggy, Spindly Growth

Legginess is the number one issue that goes wrong for beginners growing tomato seedlings or anyone in an area with low lighting. This means that the stems are elongated, spindly, and stretched out as they reach toward the light. Stems develop wimpy and leaves grow farther apart along the stem, resulting in overall weak plants. 

Solution

When something appears wrong with stem growth, the quickest fix is to move your tomato seedlings to an area with more light. If you don’t have a greenhouse or bright, south-facing window, opt for grow lights hovering just a few inches above the top leaf growth. You need to adjust the light height as the plants grow taller. 

If seedlings are already close to the transplanting stage, you can remedy leggy growth by removing one-third of the lower leaf sets and planting extra deep in the soil. This allows adventitious roots to form from the buried stem portions, yielding a stronger root system.

Wilting Leaves

Wilted seedlings are typically caused by a lack of water. Their young root zones are very vulnerable to drying out, so underwatering can rapidly lead to wilted, sad leaves. However, this symptom confuses some growers because it can also occur if there is too much water in the soil, leading to root rot. 

The key to differentiating between the two issues is checking the soil. If the soil is bone dry and the wilted leaves appear crispy, thin, and brittle, then the problem is likely underwatering. But if the soil feels soggy and waterlogged to the touch, the wilting is probably due to overwatering.

Solution

Fix underwatering by loosening the soil and gradually adding irrigation to ensure it fully infiltrates into the root zone. You can also set trays in a bottom tray filled with water to allow plants to suck up moisture from the drainage hole, gradually rehydrating the root zone.

For overwatering, stop irrigating for several days and check the drainage holes in the trays or pots to ensure that they aren’t clogged. Use your finger to loosen and aerate the upper inches of soil around the base of the plant, and monitor seedlings for signs of recovery. If the wilting doesn’t subside, you may be dealing with root rot or damping off disease.

Drooping Stems

In contrast to wilted foliage, drooping stems almost always indicate overwatering. The young plants may appear to have their “heads” down and “necks” curved over toward the soil. The excess moisture causes the stem tissues to fall over from the weight of oversaturated cells. 

In some cases, this can also be caused by long, tall seedlings growing in an overly shallow container. The top-heavy weight of the new growth may cause the entire plant to droop and flop.

Solution

Fix extreme drooping from oversaturation by re-potting your tomato seedlings in a new container with fresh, fluffy, well-drained soil mix. Be sure the pot is sufficiently deep and wide to support the developing root zone.

Check the roots for signs of rot, including mushy tissues or a foul smell. If these are present, throw the plant away and start over. If the roots are healthy and tannish-white, let them re-establish in the new container, and do not water until the stem and leaves perk back up.

Yellow Foliage

Yellowing is a generic symptom linked to overall plant stress. It could be caused by temperature fluctuations (especially cold nights), lack of light, underwatering, overwatering, nutrient deficiencies, overfertilizing, or disease. A little bit of yellowing in the cotyledons (initial sprout leaves) is common before they fall off, but an overall yellow or pale color is a sign that something more is awry. 

Solution

Check that the young tomatoes are receiving 8-10 hours of direct sunlight per day in an area with warm, 60-70°F ambient temperatures. A heating mat or row fabric can help buffer against cold nights. 

Next, ensure that the soil is consistently moist but never soggy. Monitor moisture by sticking your finger in the tray. Properly watered soil blends should feel about as wet as a wrung-out sponge.

If you spot any signs of disease, take the time to diagnose the symptoms with this guide, and treat accordingly. Prioritize gentle organic solutions such as diluted neem oil.

Lastly, ensure that your seed-starting mix has sufficient nutrients or compost blended in. If you suspect nutrient deficiencies, particularly due to yellowing and stunted growth, then add a diluted organic slow-release all-purpose fertilizer to the trays and wait about a week to see if the foliage color improves.

Brown or Burnt Leaf Edges

When your tomato seedlings appear burnt, you know something is wrong with the nutrient levels or, in rare cases, excessive bright light. In contrast to underfertilizing, overfertilizing or nutrient burn typically manifests as brown leaves with burnt-looking leaf margins. There will likely be yellow as well, but the overall “scorched” appearance hints at the term “fertilizer burn,” describing an excessive amount of nutrients overwhelming the baby plants.

Solution

Fertilizer burn is best fixed by flushing out the soil with a lot of water and transplanting the seedling to a new mix in another container. If you used granular fertilizer in a concentrated space, sometimes you can scoop it out. But if you fertilized with a potent liquid nutrient blend, the plant may need to be removed from its current growing medium altogether. 

In extreme cases of nutrient burn, I recommend throwing away the seedlings and starting over with fresh potting mix and seeds. To prevent things from going wrong, it’s generally best to avoid fertilizing tomato seedlings until you are about to transplant them in the ground.

Collapsed and Girdled at Base

You know something serious is wrong with your tomato seedlings if they suddenly and completely collapse. Damping off is a seedling-specific disease caused by fungal and oomycete pathogens. These attackers thrive in excessively wet soil. If they take hold of your sprouts, you may notice a white, fluffy, mold-like growth at the base and girdled or collapsed stems. The girdling typically occurs right where the stem emerges from the soil, eventually causing the entire baby plant to collapse and die.

Solution

Damping off is easy to prevent by focusing on four major factors:

Algae Growing on Soil Surface

Green slimy algae growing on the surface of your seed trays is a sure sign of overwatering or lack of soil drainage. This symptom may not initially show up on the plants themselves, but it will quickly affect their health in a negative way. Algal growth happens when there is far too much moisture, which can lead to more issues like root rot, irrigation runoff, damping off disease, and stunted growth.

Solution

First, use a small tool or your fingernail to scrape the algae off the surface and throw it away. Next, you’ll need to aerate the soil. If you know that the soil is already lacking drainage, you can skip this step and go straight to repotting your seedlings in a fresh, well-drained mix. 

Otherwise, you can use a fork to loosen the soil surface around the stem base. Install a fan nearby to maintain air circulation and get rid of the stagnant conditions that promoted algae growth. Hold off on watering for a few days to see if the overall appearance of the tomato improves. Try bottom watering to prevent excessive saturation from the top.

Bulls-Eye Black Spots on Foliage

Early blight is a fungal disease that commonly affects young tomato plants. It’s easy to recognize because of the “bulls-eye” shaped black spots with rings of yellow and brown. The concentric blight spots usually appear on older leaves and the lower stem first, then expand to cover entire plants, sometimes causing death. In the middle of the bulls-eye rings, there may be a sunken-in black lesion where the tissues are rotting from the fungal attack.

Solution

Once you notice this disease, promptly remove infected areas and throw them away or burn them. If the seedling is too far gone, it’s best to destroy it and start over. Do not compost any diseased plant parts, as blight spreads easily in the garden!

If only a few spots are infected, use a neem oil spray or other organic fungicide to try to combat the spread. To prevent future infections, avoid watering the leaves, choose disease-resistant cultivars, and maintain good airflow between seedlings.

Slow or Stagnant Growth

Tomato seedlings that barely seem to grow many weeks after planting may have something wrong with their fertility, light, or soil quality. Tomatoes typically grow very quickly in their initial stages. Though they take 50-80 days to start fruiting, the first few weeks should include several inches of rapid upward growth and new sets of leaves. 

Seeds typically take 4 to 7 days to germinate, and new sprouts may take a week or so after germination to reach their growth spurt. After 3 to 5 weeks, seedlings should be doubling in size every week, with several sets of lush foliage. If they appear stunted, follow a process of elimination to figure out what is hindering them.

Solution

Address and improve these key growth factors to ensure your baby tomatoes have all the resources they need to thrive:

Twirling, Tangled Roots

Roots sticking out of the bottom of a seedling tray is a sure sign of rootbinding. If you gently grasp a healthy, mature tomato seedling and pull it out of its cell, there should be minimal tangling or twirling of the roots.

If the roots are deeply knotted in the shape of the cell, it’s time to up-pot. Even if the outdoor weather isn’t warm enough for transplanting, you can prolong indoor growth by ensuring a large enough container to maintain a healthy root ball.

Solution

Carefully poke a pencil or your finger through the drainage hole of a cell tray to lift young plants out. Use your fingers to gently loosen tangled roots and up-pot the baby plants to a larger 4-or 5-inch container where they can grow until outdoor beds are ready. 

Flowering While Young

Tomatoes are not supposed to flower until they have at least 12-18” of growth and lots of lush, green foliage. The early growth stage is characterized by vegetative development, so if your seedlings suddenly shift into reproductive (flowering) mode, it is a sure sign of stress. Yellow or struggling young plants may start flowering as a last-ditch effort to reproduce because they think they are dying.

Solution

Pinch off any young flowers right away, as they suck energy away from the plant’s foliage and root development. You do not want flowers and fruit growing on young seedlings. Check that the roots aren’t rootbound, and if they are, transplant them to a larger container or into the garden.