6 Most Common/ Serious Tomato Stem Problems (and solutions)

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Quick Answer: Most Common/ Serious Tomato Stem Problems

The tomato stem gets affected due to various pathogens and environmental causes. The various tomato stem problems include bumps, dead rotten patches, wilting, stem cracking, and mold growth. It can be controlled in the initial stages using fungicide. In the worst-case scenario, you may remove and destroy the infected plants. You may use disease-resistant varieties to avoid the incidence of infection.

This post discusses the various tomato stem problems and their possible solutions.

I have encountered and tackled most of these stem problems in my tomato garden. For some, I have included the experience of my fellow gardeners.

Scroll down below for more information!

Most Common / Serious Tomato Stem Problems

Tomato stem problems may be caused due to infectious agents and various environmental factors.

It may cause bumps, brown patches, lesions, wilt, molds, and lesions. Earlier identification of the problem may help resolve the issue.

Tomato is an easy-to-grow and rewarding plant. Not only the tomato plants but their stem may suffer a range of problems that may go unnoticed.

It is important to identify these problems sooner. This subsection discusses different red flags on tomato stems that need immediate attention.

Bumps And Outgrowths

I was alarmed when I observed white bumps or growths on my tomato plants.

But, these are just roots. It starts as tiny hairlets called nodules that become roots if buried underground.

These bumps form on the tomato stems due to stress. It may be because of root damage, injury, irregular cell growth, and overwatering.

Another reason for this bump may be herbicide exposure. In such cases, you may check for curled or stunted leaves that accompany the bumps on the stem. Sometimes, it may be caused due to diseases.

In most cases, these bumps are harmless. If the issue is overwatering, you may drain the excess water. The tomato plants may revive back after fixing the stressors.

It may be difficult to save the tomato plant if it is attacked by pathogens.

Here is the video for more information about bumps on tomato plants:

Black Spots Or Dead Rotten Patches

Many diseases cause black spots along the tomato stems that is alarming. It needs immediate attention to prevent the spread of infection.

The stems of tomatoes may develop brown, rotten patches when attacked by the fungus, Didymella lycopersici. The condition of Didymella stem rot first affects the base of the stem.

It then attacks the upper parts of the tomato stems.

Early blight is another disease caused by fungi, Alternaria solani. The symptoms include dark brown or black spots on the tomato stem above the soil.

It is a commonly occurring problem that may be tackled using a fungicide.

Another fungal disease that thrives in humid climates is late blight. It spreads fast from purple-brown spots to black lesions and from leaves to stems.

Many gardeners recommend pulling the plants affected by late blight. It is more damaging than early blight.


If you observe the lesions on the tomato stems, it may be due to Alternia stem canker or bacterial canker. These conditions may be hard to cure.

I haven’t come across Alternaria stem cankers, but few gardeners have experienced it. Dark brown lesions appear on the stems that slowly spreads to the fruits. The wet conditions accelerate the spread of infection.

Bacterial canker is another tomato disease that causes black spots, brown streaking, and dark lesions. It is caused by Clavibacter michiganensis.


Sometimes wilting occurs inside the tomato stem with staining. It may be associated with Verticillium wilt and

Fusarium wilt.

If the stem is cut transversely, Verticillium wilt is visible as a circle of brown marks. It appears as brown streaks if cut lengthways.

Another fungal disease caused by Fusarium oxysporum is Fusarium wilt. I did not observe any soft decay on the tomato stem.

But when I cut the stem lengthwise, there was dark brown discoloration of the water-conducting vessels. It later caused wilting of the plant.

White Spots And Grey Molds

Another tomato stem problem that I have faced is white mold, timber rot, or sclerotinia stem rot. It is caused by fungi, Sclerotinia sclerotiorum.

The prolonged cold and wet conditions may worsen the spread of infection.

First, the watery soft rots appear on the main stem of the tomato plants. Next, a white fuzzy mold grows inside and outside the plant.

It then spreads to the whole plant, and it will start wilting. Even the fruits start turning gray and rot.

Also, these mold fungus releases spores that may be carried by the wind and attacks the neighboring plants. I had to remove the infected plants immediately to avoid the spread of fungi.

Check out this video for more information on white mold:

Occasionally, I have encountered grey mold caused by Botrytis cinerea. The fungi enter the stem through the wound. It spreads under humid conditions and expands to the entire stem causing wilting.

Stem Cracking

Some of my tomato plants had small skin cracks on the stem. It was vertical and was not spreading. I identified that it was due to strong wind causing pressure on the tomato stem.

It may also occur due to extremities in temperatures.

It may also be due to rapid growth accompanied by water inconsistencies. If there is a heavy downpour, the plant may take excess water through the stem. It creates pressure causing the stem to split vertically.

Sometimes, cankers and exposure to herbicide create a necrotic spot on the tomato stems. As the living part of the plants continues to grow, pulling the dead spots, the stems may split open.

I solved the problem by holding the plant straight and attaching it to support. I also corrected the overwatering issue.

How To Fix Tomato Stem Problems?

The tomato stem problems may be corrected by applying the fungicides and correcting the watering problems.

You may sanitize the garden tools, check for pests, and choose the disease-resistant varieties. You may remove the infected plants and destroy them.

It is important to identify the cause of the tomato stem problems and rectify them as soon as possible. Also, you may follow certain preventive measures mentioned to avoid the occurrence of such problems in the future.

  • I prefer to choose healthy, disease-resistant plants. If using seeds, you may get them from certified sources.
  • You may check for any pests. Crop rotation is another way to reduce infections.
  • You may water the plants at the base of the plants. Ensure proper drainage system.
  • Allow good air circulation around the plants to keep the foliage dry and prevent infection. Also, avoid overcrowding to prevent the disease from spreading to tomatoes.
  • Remove and burn the infected plants to prevent the spread of infection.
  • Solarize the soil at the end of the season to destroy the soil-borne pathogens.
  • Sanitize the garden tools and equipment before use.


How can we control tomato stem rot?

Fungicide treatment may be effective if sprayed in the earlier stage. However, preventive measures are the best way to reduce the occurrence of tomato stem rot. You may use healthy seeds or disease-resistant varieties. If the infection is fast spreading, it is better to remove and destroy the plants.

Why is my tomato stems turning black?

The tomato stems may turn black due to an attack by fungus. The different causes may be Alternaria stem canker, bacterial canker, early blight, and late blight. For best management, the fungicides may be sprayed before the plants show signs of infection.


It is a wrap on different tomato stem problems. I hope this informative guide helps you to identify and solve tomato stem issues.

Let us know your suggestions and write back to us with any queries. Also, we would like to hear about your experience in dealing with tomato stem problems.

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