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Tomato Seedling Problems [With Quick Fixes]

Do you know fresh tomato seeds have around 90% germination rate success, sprouting easily without any issues?

But once they mature into tomato seedlings, they may face many muddles along their growth course! 

Common tomato seedling problems include droops and wilts, color changes (purpling and yellowing), slow growth, visible white patches, brown leaves or spots, legginess, fungal and viral attacks, and improper hardening methods.

To cater to these doubts about tomato seedling problems, let us go through the possible causes and solutions.

10+ Tomato Seedling Problems [With Solutions]

Growing tomato seedlings from seeds take at least 6-8 weeks from sowing to transplanting.

However, it takes about 4-14 days for tomato seeds to sprout when provided with conducive conditions.

Further, these conditions include water sprays twice a day and a constant temperature of around 65-85°F until germination.
Image illustrates true and developing leaves of tomato seedlings
You can thin out tomato seedlings after they develop at least 3 sets of true leaves.

Once 25-35 days into the early growth stage, tomato seedlings gain a true set of leaves and roots sturdy enough for transplanting.

Hence, they must be looked after like mature tomato plants.

Without proper care, tomato seedlings face many problems, which we will discuss along with their causes and quick solutions below.

1. Droopy or Wilting Tomato Seedlings


  • Overwatering during fall and winter – soggy soil, lack of oxygen within the potting environment, and root rot
  • Underwatering during spring and summer – arid soil, inability to transport nutrients, and lack of water for the tomato seedlings


  • Water daily with 0.3 inches and 1-2 inches weekly during spring and summer.
  • Refrain watering during fall and winter to prevent the seedlings from drowning.
  • Check the top 6-8 inches of soil for dryness before watering.
  • Amend the soil with porous ingredients like organic perlite to increase drainage.

2. Purple Tomato Seedling Problem


  • Potassium or phosphorous deficiency – reddish-purple leaves and veins
  • Viral and pest infestation – weak and droopy leaves
  • Leaf burns – browning or purpling of leaf edges and tips


  • Opt for high potassium and phosphorous-rich fertilizers weekly in spring and summer, or incorporate the soil with bone meal.
  • Prune diseased parts or discard the whole plant in case of severe viral diseases like Tomato Mosiac Virus (ToMV), Cucumber Mosiac Virus (CMV), and Tobacco Mosiac Virus (TMV). 
  • Protect the seedlings from direct sunlight and keep them in a shady spot for a few days to recover.

3. Stalled Growth Rate


  • Close spacing – competition between the seedlings for nutrients, light, and water
  • Weak sunlight – less photosynthesis and energy production for vertical growth
  • Low and high temperatures – less foliage and flower production
  • Lack of humidity and moisture – foliar contraction
Image represents overcrowded tomato seedlings
Overcrowding causes competition between the tomato seedlings for nutrients, water, and light.


  • Keep at least 1-2 feet of space between the seedlings while planting.
  • Offer at least 6-8 hours of sunlight daily to the seedlings.
  • Place the seedlings on heating mats maintained at 65-85°F.
  • Maintain ambient humidity of around 65-90%.

4. White Patches On Tomato Seedlings


  • Extreme humidity with poor air circulation – powdery mildew stirring white patches on leaves
  • High nitrogen or phosphorous in the soil – whitish-brown discoloration triggered by fertilizer burn
  • Extreme heat or cold stress – sunscalding of exposed parts (leaves and stems)
white spots on tomato leaves
Sunscald causes whitish-patches to appear in the surface of the leaves.


  • Maintain a relative humidity of around 60-85% using humidifiers or humidity trays.
  • Use fertilizers with less nitrogen or phosphorous, or halt feeding until the symptoms subside.
  • Protect the seedlings from cold stress using frost blankets in winter.
  • Use fresh potting mix and repot the seedlings to discard the pathogens from old soil.

5. Brown Leaves or Spots


  • Imprudent or underwatering – visible brown patches on the tomato leaves
  • Early blight – concentric brown spots or blotches on the leaves due to acute soil wetness


  • Prevent overhead watering and maintain a porous potting environment.
  • Prune off infected leaves and use foliar fungicides to tend the seedlings.
  • Permeate holes on the topsoil to offer a boost of drainage for the plantlings.

6. Yellow Leaves On Tomato Seedlings


  • Nitrogen, potassium, and magnesium deficiency – entire or older leaves turning yellow 
  • Lack of oxygen in the soil – mushy soil due to overwatering suffocate the roots
  • Transplanting stress – inability to adapt quickly to a new potting environment


7. Leggy Tomato Seedling Problems


  • Lack of natural or artificial lighting – leaves and stems stretching towards the sunlight source
  • Crowded and warm growth conditions – foliage unnecessarily extending for bright light
  • Erratic watering and high fertilizer use – extensive stem and leaf length due to overnutrition
Image represents leggy tomato seedlings
Low light and crowded conditions causes the extension of leaves and stems.


  • Situate the seedlings about 6-12 inches away from the grow lights for 12-16 hours daily to cope with the lack of sunlight.
  • Maintain spacing between the seedlings or trim some spent leaves to improve airflow.
  • Avoid using fertilizers that improve the foliar appearance of the plant or dilute the fertilizer for minimal use.

8. Curling and Brittle Tomato Seedling Leaves


  • High summer heat – soil moisture loss and shriveling of plant leaves (physiological leaf roll)
  • Die backs – leaf burns and expulsion of water from the tissues 
  • Curly tops – rolling or bending of top leaves


  • Keep the seedlings in a shady spot to revive the wilted leaves.
  • Maintain ample soil moisture and keep the soil damp but not soggy during summer.

9. Black Fungus


  • Tomato leaf mold – the appearance of yellow patches and black fuzzy spots on the leaves
  • Honeydews left by pests – a suitable breeding ground for sooty molds


  • Install sticky traps around the plantlings to slay hovering pests like whiteflies and thrips.
  • Use Q-tips laced with neem oil to wipe out the visible pests from the seedlings.

10. Fungal Disease Problems


  • Botrytis: Patches of black decay on leaves and stems
  • Damping off: Droopy and yellow foliage


Image represents yellow tomato leaves
Sudden transplant can cause the tomato leaves to turn yellow as a sign of stress.

11. Abrupt Seedling Hardening


  • Relocation or transplant stress – yellow leaves and droopy leaf stalks with stems


  • Begin hardening tomato seedlings when they are about 1 month old.

From Editorial Team


Tomato seedlings are delicate and must be given the correct warmth, temperature, light, and watering during their growth phase.

Hence, they need frost protection if you grow them indoors during winter and later transplant them in warm soil at 65-70°F. 

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