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Bonsai Root Pruning

How to Prune Bonsai Roots? A Detailed Guide for beginners

In bonsai culture, the riskiest part is pruning the roots, especially if you are a beginner. 

So, let me guide you through the steps of pruning bonsai roots and hopefully take away your fear.

Any plant’s roots, especially a bonsai tree, are crucial. In normal circumstances, it’s not visible to your eyes, but it serves as the most important part of the plant for it to survive.

Bonsai root pruning is a bit different from pruning tree branches. Because in the bonsai tree, results are happening underground, but you can see the effect above the ground. Hence, there is quite a lot of consideration while pruning the roots of your bonsai tree.

Why prune roots?

why prune roots

While growing any plant in the container, you have to work on the roots from time to time. Roots grow more than the stem in any natural habitat, searching for nutrients and water.

But when you confined the plant in a container, the situation became different because roots cannot grow as much as they like.

The limited space causes roots to get colonized in a particular container area. So, if you do not prune the roots, the container becomes oversaturated with roots, and this condition is called root-bound.

And when this happens to the plant, it suffers immensely and eventually dies. At that time, no amount of branch or leaf pruning will solve this problem. So, sooner or later, you have to prune the roots and needs to transplant them to a larger container.

Bonsai pots are an essential part of the bonsai tree’s presentation. They come in various shapes, sizes, and materials like ceramic, plastic, and clay. Buying bonsai pots online can provide access to a wide range of options suitable for different types of bonsai trees. It’s important to choose a pot that is the right size for the tree and complements its overall aesthetics. 

Why root pruning is a must for bonsai?

In bonsai culture, the main goal is to keep trees in a miniature form. Therefore, pruning of roots, stems, leaves, and regular plant repotting, are needed.

When you prune the roots, it stimulates the growth of many smaller roots, which is crucial for the look and survival of the plant.

Bonsai trees are not like natural plants because they don’t need taproots to survive. The primary purpose of the taproot is to provide an anchorage for the plant. A bonsai, however, has been given support from the outside when it is wired.

Additionally, a thick taproot can suppress the growth of any smaller roots, which can lead to sparse branches with relatively little foliage.

Therefore, root pruning is a must for a bonsai tree. This is an integral part of creating different styles of bonsai.

How often do you need to prune roots?

The frequency of root pruning in bonsai depends on a few factors, such as plant species, container size, and environment, in deciding how often pruning is needed.

If your bonsai container is small, the bonsai trees will colonize the container very fast with roots, and you might need to prune the roots every year lightly. Whereas in a larger container, it takes time to get to that situation.

Some tree species are slow-growing and may not need frequent root pruning. Besides, you might have to do it quite regularly for other species to maintain their vigor.

Moreover, bonsai root trimming is also done when the bonsai tree shows the symptoms of chlorosis, decline, or push out of the container because of abundant root growth.

When to prune bonsai roots?

Whenever you prune the plant’s roots, it stresses out the bonsai plant. Moreover, roots are the plant’s lifeline, so when bonsai root pruning is done, the plant must adjust to the shortage of water and nutrient intake.

Therefore, the timing of root pruning should be when the bonsai is under the least stress, such as during a period of dormancy (for tropical plants) or early spring.

The ideal time to trim bonsai roots is in spring, just when roots begin to grow. If done earlier, such as in winter, the wounds created will remain open for a longer duration and will be vulnerable to the risk of further damage, such as from frost or fungal attack.

You can notice the first sign of root growth by seeing the swelling of the buds at the shoot ends.

Moreover, the stress on your bonsai plant will be minimal in the spring because of the low transpiration rate.

Tools you need to prune bonsai roots & how to do It

Bonsai root pruning toolsUse
SpatulaTo firm down the bonsai soil
Jin piler and wire cutterRemove wires that bind the tree into the pot, replace them with new wire ties, and tie the bonsai into the pot.
SickleTo cut the bonsai out of the container
Plastic brushTo clean bark
Metal brushTo clean bonsai container 
Coco brushTo tidy up the surface of the container
Root cutter IFor cutting finer roots
Root cutter IIFor cutting heavier roots
Metal chopstickFor clearing the root surface.

First, start to unpot the bonsai plant once you remove the bonsai plant from the pot. Comb the roots radially using a root hook.

A root hook helps to untangle and straighten roots without damaging them. So, you can either purchase these or make them yourself. Alternatively, use a chopstick to untangle your plant’s very small roots.

You must be lured by the idea of blasting the root ball with water and removing all the old soil. Although this might be helpful for some species, it causes harm to fine root hairs.

There are two types of roots: The Taproots and Fibrous roots, also known as thread roots. Usually, pruning of Fibrous roots is done for root bounding.

It would help if you pruned the larger thick roots of the bonsai because small roots are more efficient at absorbing water and nutrients; after all, these fibrous roots are vital for a plant’s survival after bonsai root pruning.

If you convert a regular plant into bonsai, then much root pruning is needed.

In bonsai, the root system is substantially shallower than any nursery plant. Therefore, nearly 1–to 5-gallon pot must be removed from most lower portions.

Moreover, it is not advisable to directly move any nursery plant into a bonsai pot. You need to do this by gradually shifting them to smaller pots. After a year or two, you can do further bonsai root trimming and shift them to a bonsai pot.

While cutting roots, be a little careful but do not get scared. Pick carefully. To be on the safe side, do not cut more than ⅔ of the roots of a pot. Start trimming conservatively, and as you gain confidence, you will move to more severe bonsai root pruning.

After that, remove the taproot remnants under the crown and any circling roots. Prune the roots all around so you can easily fit the bonsai in its new pot. Try to keep fine roots intact.

As you have completed the bonsai root pruning process, prepare the pot where you would like to place your bonsai tree. Make a shallow layer with the soil and place the root ball on top of that shallow layer.

Next, fill the soil into the spaces between roots. Also, check that there is no air space between them. Use the chopstick to keep poking the soil until there is some resistance to ensure no air pocket and the soil is filled.

Last but not the least, water it deeply. You need to do watering carefully. Because watering (as it sinks in) may reveal where you need to add just a bit of soil.

Water a couple of times, to settle the soil and wash out the fine materials.

How to prune roots when transferring a bonsai tree from a nursery pot to a bonsai pot 

It is impossible to prune the bonsai tree’s roots down from the length they were in the nursery pot you purchased to the length they need to fit into the final bonsai pot all in one go. 

Making a transition too quickly will damage your plant.

Instead, you should adopt a gradual approach. Prune your root ball down as much as you can. Make sure not to hurt the tree; then, repot them into a shallow training pot.

Also, while pruning, you should not remove more than ⅔ of a bonsai root system at once.

How soon you can prune your bonsai roots down to the size to fit comfortably in the final pot depends on the timeline of the bonsai.

For instance, purchasing the 5-year-old tree will take less time to get it into the final, shallow pot container than seedling yourself.

What do you need to prune off?

  • Prune away roots, large and small, growing straight down.
  • Roots that grow above the chosen line of the root surface.
  • Roots that are crossing radial emerging roots from the trunk


1. How do I know if bonsai is root-bound?

The sign of root-bound is the circling of roots around the root system.

Several tell-tale symptoms show a plant has become rootbound. The issue is that this problem is usually confused with underwatering. Without scooping up a plant from the pot and examining its roots, it’s actually very easy to detect it.

Root-bound plants normally have symptoms such as withering that happens all of a sudden. They can also display brown or yellow leaves, usually around the lower parts of the plant, and stunted maturation. It could also force a pot to be pushed out of shape or even broken by the roots.

If you see roots forcing further the soil surface, that’s another sign. This shows that your plant has developed way too much for its pot.

Anyways, the best method to know for certain that your plant has bound roots is to examine the roots itself. You’ll have to pull the plant from its container to do this. Take in mind that poorly root-bound plants will be quite challenging to pull from their containers.

This is why these days, most gardeners use garden pots with holes at the base. When you see roots peeking through these holes, you’ll get a head start that your plant has outgrown and is about to be root-bound. This is a cue that it’s time to re-pot. 

2. How to grow a bonsai trunk thicker?

Allow the tree to grow freely in a large pot without pruning it for years. Once you are satisfied with the trunk thickness, you can train it again and place it in a small pot.

3. Should I cut the dead branches of my bonsai tree?

Always remove dead bonsai branches. Because dead branches carry disease that passes to the rest of the tree, eventually killing your bonsai tree.

4. Can I use normal scissors for the bonsai trees?

Normal scissors are blunt. At the same time, Bonsai scissors have sharpened blades. The sharpened blades cut rather than tear. So only if you have scissors that are sharp like blades can you use them.

5. Should I prune before or after repotting?

Prune the roots and loosen up the root ball before repotting for good nutrient absorption. You can use a sharp knife or pruning shears for this work; remove as much as the bottom third of the root ball, if necessary.

6. What to do after root pruning?

You should give your plant time to take rest. Now that your root-bound plant has been root-pruned, watered, and even leaf-polished, it should take a rest. If your plant is usually living in a medium to low-light space, you can move ahead and place it back in its original space. But, if the plant you’ve root pruned is a plant that typically lives in plenty of direct or indirect sunlight, you’ll be required to provide it a week or two pause and place it in a spot with partial shade, before replacing it to its actual location. Plants too require time to cure after “significant interventions”.

7. What are the disadvantages of pruning?

If pruned too early, too many buds will grow and next year’s maturation will be disfigured. If pruned too late, your tree or shrub will be stunted. Pruning cuts should be created on the present year’s development. Pruning into 2-year-old wood, delays bud building for one year.

8. How to prevent root-bound?

Instead of instructing you how to repair root binding, why not instruct you how to control it? Scrutinizing your plant with the detection methods will work best, but if you are a forgetful owner of a plant, I have another way to suggest. 

Plastic pots. Yes, plastic pots have been the choice for new plant owners for some time. But nowadays, you’re more suitable with a more breathable material like fabric pots. These kinds of pots allow for oxygen to penetrate the root zone. Once your plant roots hit the fence of the container, the air prunes them and controls additional growth. On the other hand, plastic pots let no oxygen into the root zone and create situations where the roots grow across themselves and tangle. 


Growing a bonsai tree is a labor of love, and part of the process is bonsai root trimming for the healthy growth of the roots and overall plant. Bonsai root pruning is important because it helps the bonsai tree maintain its miniature shape and allows the young, absorb, and viable roots to grow.

However, pruning bonsai is a precise task, and you need to know when and how to perform bonsai root pruning to keep your tree healthy.

I hope this article helps you prune your bonsai tree’s roots successfully. Please share your first experience with bonsai root pruning in the comment section below.

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