It can be frustrating when the plant you’re growing starts getting a black stem and you have no idea what’s happening.

Your plant stems are turning black because they are suffering from stem rot that is caused due to fungal diseases such as blight or bacterial wilt. The stem could turn black temporarily due to environmental stress such as intense heat or cold or even transplant shock.

If you want to figure out what’s going on and the solution to the problem of your plant stems turning back then keep reading.

Hot weather

The most common problem for plants is hot weather especially if they are plants that cannot deal with extreme heat.

A sharp temperature rise will cause the stems and leaves of some plants to start drying and wilting. A side effect of this problem is they may end up with a dark brown or black appearance.

The good thing about this problem is it’s temporary. As soon as the heat reduces, the leaves and stems will come back to their normal color. There is no harm done to the plant.

You can also help by shading the plant with a row cover in such a situation. If you’re growing in a container, it’s easy to move the plant to a shaded location.

Transplant shock

You may have started seeds indoors, and they have developed into seedlings. Or you may have bought the seedlings from a garden center or nursery.

If you don’t harden the seedlings before the transplant to the garden, they can suffer from the problem of transplant shock.

This happens because the plant cannot handle moving from a comfortable indoor environment to a harsh outdoor one. It cannot bear the intense sunlight and wind that may fall on it.

The transplant shock may stunt the plant’s growth. It may have droopy leaves and the stem may change color to appear black.

The solution to this problem is known as hardening. Before you can transplant the seedling outdoors, get it used to the environment.

You can keep the seedling outside for a few hours every day and bring it back in. Make sure to keep it away from direct sunlight, wind, and rain when hardening.

Keep doing this every day and your plant will be ready for the transplant after a week.

Fertilizer burn

One of the needs of many plants is the nutrients you provide to them in the soil. You may need to add fertilizer when the soil does not naturally contain them.

The problem may happen that you add too much fertilizer especially synthetic ones. And the plant will tell you this problem with fertilizer burn.

The overload of fertilizer will literally burn off the roots of the plant. The problem will also spread to the stem causing it to turn black.

I always recommend using compost in your soil as that is natural and will give the best nutrients to the plant.

If you do have to use fertilizer, choose an organic one that has fewer chances of overwhelming the plant.

But regardless of choosing an organic or synthetic fertilizer, make sure to follow the manufacturer’s instructions. It will tell you the amount of fertilizer to use and how often it has to be added.

If the plant has already suffered from such fertilizer burn, you can take it out of the soil and cut off the affected roots. Move the plant to another location in the garden that has fresh soil free from such fertilizer.


Overwatering is one of the most common problems faced by gardeners, especially when we have just started to grow plants.

It can be an innocent mistake because you just want to give the plant water and protect it from lack of water. But it’s also a dangerous mistake that can kill your plant.

Overwatering will cause the roots to drown in water and invite problems like root and stem rot. This disease will slowly kill the roots and stem.

The roots will start to turn black, soggy, and slimy. Slowly, the problem will move up from the roots to the stem as well turning it black.

One of the reasons for overwatering is that the soil does not have good drainage. You need to make sure of the drainage when preparing the garden bed.

If the soil is too full of clay, it won’t drain well. You need to either amend the soil to improve its texture or you need to use a raised-bed.

If you’re growing the plant in a container, make sure it has several drainage holes at the bottom.

Different plants will need a different amount of water. But the best way to know the moisture in the soil is to use your finger.

Stick it in the soil 2-4 inches deep and if the tip of your finger feels moist, you should not water the soil.

If the stem has turned soggy and black, you should dig out the plant and check the roots as well.

If all the roots are soggy and black, you can’t save the plant and need to dispose of it. If only some roots are affected, you can cut them off.

Move the plant to another location in your garden that has clean and dry soil. Monitor it for a week and check if the stem returns to normal health.

If it does not heal itself, there’s not much you can do but dispose of the plant.


There is no garden in the world that was not infected by disease at some point. And your plants will also face this problem.

Some of these diseases will cause the stems of your plants to change color and turn black or brown.

The best way to avoid fungal diseases is to protect your plant from a humid condition. Make sure you don’t spray water on the foliage when watering the plant.

Keep the plant pruned so there is good air circulation in the foliage to prevent a humid environment.

To protect your plants from bacterial infections make sure to clean the tools before using them on the plant. Use rubbing alcohol that will sterilize the tool.

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

Some of these diseases are carried to the plant by pests such as aphids and whiteflies. Make sure to attract beneficial insects that will get rid of such pests. You can grow native plants to attract such insects to your garden.

You can also apply neem oil to your plants every couple of weeks to protect them from some bacterial infections.

Viral diseases are quite bad for the plant as there is no recovery from them. You can only slow down the problem but eventually, the plant will die.

The best solution to protect your plant from viral diseases is to try to find a cultivar that is resistant to them.

I’ve listed down some diseases that can cause the plant stems to turn black.


Blight is a fungal disease that can reach your plant through gardening tools or insects like aphids and beetles.

The fungal spores may activate when there is a humid condition caused due to water on the foliage.

This fungus will affect different parts of the plant including fruits, leaves, and the stem. It will leave a gummy, black residue on the stem.

The best you can do is prevent this disease from reaching your plant. Keep water away from the leaves and stem of the plant. Keep your gardening tools sterile using rubbing alcohol before use.

Make sure to use seeds that are resistant to blight. If the disease has started on the plant, there may be some fungicides that could solve the problem.

If there is a severe infection on the plant, you may have to get rid of the entire plant.

Black spot

Black spot is another fungal disease that can affect the leaves and stem of your plant. The disease starts with small black spots that grow larger till the leaves fall off.

Like other fungal diseases, this can reach your plant if the foliage is wet after you water the plant. It can also be carried over by wind and insects.

The best solution is to prevent a humid condition from developing on your plant. Avoid splashing water on the leaves and stem.

If the plant is infected, you can use neem oil or insecticidal oil spray on the plant. Keep applying it every week till the problem goes away.

organic neem oil
Organic neem oil I use on my plants

You can also find organic and synthetic fungicides that will get rid of this problem from the plant.

If the entire plant is affected by the disease, it’s best to get rid of the plant. Make sure not to grow plants in the same soil for a few years as the spores may remain there.

Stem canker

Stem canker is another fungal disease that affects some plants causing the stem to turn brown or black in color.

Small lesions start on the stem as the plant is young and mature into black colored large lesions. Once the lesions mature they will prevent nutrient and water circulation in the stem and cause the plant to die.

Like other fungal infections, this disease will infect the plant in humid conditions caused due to water on the foliage. So it’s best to water carefully so it only goes to the soil.

The other way to prevent this fungal disease is to use a resistant cultivator. Once the plant has been infected, you can use organic or chemical fungicides to get rid of the problem.

Pith necrosis

Pith necrosis is a bacterial disease that will cause the stem of the plant to grow black lesions.

This is a disease that will infect plants when the temperature drops and humid conditions are present. It can also become active when excess levels of nitrogen are present in the plant.

It will cause wilting of the stems to begin. And later the color of the stem will change to black. When you cut the stem, the center or pith of the stem will be discolored or hollow.

The best you can do is to keep the plant away from humid conditions and temperature drops. Avoid spraying water on the foliage and keep the plant warm at night with a row cover.

Make sure that there is no excess nitrogen supply to the plant from the soil or the fertilizer that you use.

There is no treatment available to rid the plant of this disease. But if the infection is less, you can nurse the plant back to health and recovery.

Leave a Reply

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.