Bonsai Health Issues: Why is my Bonsai Trunk Squishy?

  • By: Josh Koop
  • Date: July 10, 2022
  • Time to read: 6 min.
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If you are a beginner at bonsai, you have a lot to learn about taking care of bonsai trees. You may have been watering, fertilizing, and providing sufficient sunlight for your bonsai trees . But you noticed that one of your bonsai trees has a squishy trunk. So, you are wondering: why is my bonsai trunk squishy?

A squishy trunk on a bonsai is one of the few symptoms of bonsai root rot. The tissues under the bark of the trunk are dead, and so it gets mushy. This problem does not occur overnight. It can happen because of continuous over-watering of the tree. 

A squishy trunk is a serious problem that can eventually lead to the death of a bonsai. However, you can still save your bonsai by taking immediate action. Keep reading this article to learn how to fix root rot and avoid the problem in the future. 

How To Know Bonsai Root Has Rot?

Bonsai trees have different species, sizes, and designs. Besides, they can have different sizes of pots and types of soil. Hence, the trees require a different amount of water. Beginners often over-water their bonsai trees, which results in root rot. 

Root rot can occur in both outdoor and indoor bonsai plants. It can be caused for various reasons. Over-watering and poor soil quality are the main causes of root rot. Besides, it can happen due to insufficient light and fertilizer. The root system of the bonsai gets less oxygen and eventually decays. 

A squashy trunk is an indication of root rot in a bonsai plant. There are a few other symptoms of root rot and overwatered bonsai. The leaves of the bonsai tree drop. They may turn yellow, and the tips may become black or brown. The smaller branches shrink, giving the tree a dull look. 

Since bonsai trees have shallow roots, you can easily check the roots by removing the bonsai from the pot. If the tree comes off the soil freely without much resistance, it means the root system is weak. Healthy bonsai roots have a firm grip on the soil and look white. Unhealthy or rotten roots appear brown and become soft. 

All the symptoms prove that the bonsai has been suffering for some time , and damage has already been done. If you want to save your bonsai, you must take the necessary steps as soon as possible. With proper care, it is possible to make your bonsai healthy again

How To Fix Bonsai Root Rot?

Now, what can you do about bonsai root rot? Reviving the dead roots back to life is not possible. So, first, you need to check how much of the root system you can save. Use a toothpick to remove soil from the roots. If the entire root system is squashy and soft, it means the entire root system is dead and you won’t be able to save your bonsai.

However, if you have some white firm roots, you have the chance to save the bonsai. For that, remove the dead roots and re-pot the bonsai . Here is how to remove the damaged roots and repot your bonsai:

  1. First, remove the bonsai from the pot. Do not rush while removing the roots. If your bonsai was stuck on the pot with a wire, remove the wire first.
  2. Then clean the soil from the roots with a toothpick or root rack to check the damage. Start by removing soil from the side and bottom of the bonsai. 
  3. Take a sharp pair of scissors to cut off the dead roots. If you find roots partially damaged, cut off just the damaged parts. Leave behind the healthy parts.
  4. Now, you can re-pot a bonsai in the same pot or get a new bonsai pot. 
  5. In case you want to re-pot in the same pot, you have to properly clean the pot. Remove any green spot or dirt thoroughly and sterilize it. 
  6. Next, cover the drainage hole with a piece of mesh. It will keep the soil from draining out, and the roots coming out through the hole. 
  7. Then attach the wire to the pot, which you will use to anchor the bonsai
  8. Next, fill up the pot with new soil. The soil has to be bonsai appropriate, which means it should drain the excess water to the drainage hole. For that, the first layer of the soil has to be heavy grain soil such as grit, lava rocks, or akadama. 
  9. Add a thin layer of bonsai soil and plant the bonsai on it. Attach the tree on the pot with the wire. After that, add another layer of bonsai soil around the tree to cover the roots. 
  10. Make sure there is no air pocket around the roots. You can use a toothpick to set the soil around the roots. 
  11. Finally, water your bonsai thoroughly. Check if the drainage hole is blocked and if the excess water is coming out. 

The root pruning will help the healthy roots grow and create a new root system. After a few days, you should find your bonsai thriving. 

How Often Should You Water A Bonsai?

To prevent root rot in bonsai trees, avoid over-watering them. Typically, bonsai trees need to be watered once every four to seven days. There are different species of bonsai . They do not require the same amount of water. So, you need to learn about the species of your bonsai . During extreme heat, some species may require watering every day. 

Besides, outdoor bonsai trees that get more sunlight will require more water than indoor bonsai trees that stay at cool temperatures. 

Both under-watering and over-watering are bad for your bonsai. If your bonsai tree does not get sufficient water , the leaves will become wilted and fall off. On the other hand, over-watering results in root rot. 

So, you need to know the right time to water your bonsai. You can check the moisture of the soil with a soil moisture checker or just stick your finger in the soil. If it feels dry , water the bonsai. But it still has some moisture; there is no need to water it even if a few days have passed. 

What To Do If Bonsai Is Overwatered?

Sometimes, you think you are caring for your bonsai by watering it every day . But you are actually harming your precious plant. You may realize later that you have been over-watering your bonsai for some time now. So, look for the symptoms of overwatering and root rot. 

If the leaves are yellowing and droopy or the trunk is squashy, check the root of the plant. When the symptoms appear on the upper part of the tree, there is a strong possibility that the roots have already been affected. Hence, follow the steps mentioned above to solve the problem.

However, you may not see the symptoms but find the soil wet for days. In that case, avoid watering the plant for a while until the soil gets dry. Check the moisture from time to time. Make sure the extra water drains out of the pot. Check the holes under the bonsai pot. They might get clogged, so clean them to let water out. 

Also, it is important to re-pot your young bonsai plants every two years and the older ones every three to five years. By this time, the bonsai trees have used up all the nutrients in the soil. Besides, the soil loses the ability to drain water properly after years of use.  


By now, you should have the answer to the question: why is my bonsai trunk squishy? Now that you know that over-watering is the reason for a squishy trunk, you should stop the practice. By taking the steps mentioned in this article, you can bring your bonsai back to health. 

In a few days, you will find your bonsai healthy and beautiful again.