Starting A Bonsai From Seed – A Guide For Years 1 To 5

Starting a bonsai from seed is one of the most rewarding things you will ever do, but be warned it is also one of the slowest and longest tasks you will ever undertake. 

I’m not going to go into how to germinate seeds here as there are a number of different techniques all dependent on what species you are growing. 

I’m just going to give you a general overview for what you should be doing for the first couple of years, which to be honest isn’t much …like I said, it’s slow.

After Your Seed Has Germinated

Once your little seed has popped its head above the soil, what do you do next? Well. Sadly the answer is to pot it up and wait for it to put on some growth. 

What Size Pot Do You Put A Seedling In?

The pot size matters, but it also doesn’t matter, Basically just put it in anything you have for no. If its too small its fine, you can up pot it later, if its too big, well it will grow into it and you can down size the pot later if you want. The main goal here is to just get the tree growing and to get it health.

So the basis of any good bonsai is it that needs a good trunk. The only way you can get this is through lot of growth. I go into in more detail in this article – How to speed Up A Bonsai.

Basically a seedling needs to grow big and tall to get any sort of thickness. However, to grow, a plant needs room to stretch out. It needs to spread its roots out and the bigger and longer it’s roots get, the bigger and longer it’s branches will become.

Simply put, a tree needs space and well a 2 inch mame bonsai pot isn’t exactly a lot a space. if you want your tree to be large then you need to use a large plant pot, or even the ground, where it’s effectively got unlimited space to grow. 

Now, on the other hand I understand that space isn’t an option. I myself began in a small flat in London.  No access to outdoors. No room for a large plant pot. So I stared loads of seeds in very small pots.

I used yoghurt pots, small plant pots and even bonsai pots. It was either do that, or do nothing. I would always rather you grew in small pots and take 10 times longer than not even try because you haven’t the space to fit a large pot.

Obviously the ground is the best option! But not everyone has that option. (Read more about Growing In The Ground)

Can You Use A Bonsai Pot?

A lot of people frown on this, as a seedling is not a bonsai. However I have done it as it was all the space I could accommodate.

Maybe you are growing your tree in a 2 inch mame pot as that’s the size of tree you want. Not everyone wants a meter tall juniper that takes 3 people to lift. 

I would still say to try and pot your tree in a flower pot. Even for a year. That year alone in a slightly bigger pot will give you a great size and it will be perfect for your smaller mame pot after a year. To start the tree in a bonsai pot may take it 5 times for it to thicken to the size you want. 

If you watch any of the videos I have made where the tree is grown all its life in a bonsai pot, you will see that after 5 years they are still small and pathetic, compared to those ones allowed more room to grow.

Basically just got for the largest pot you can and wait. For the first year you shouldn’t even touch the tree. Just care for it and let it grow as much as possible. I know you want to start pruning and styling, but you have to be patient. The tree isn’t ready for any of that yet.

After The First Growing Season

At the end of the first year, in late winter you can start having some fun. But let me just say, it’s probably going to be a short lived fun.

I would start using my basic pruning techniques to prune your tree. 

However, a year old seedling isn’t really going to be big enough to need to have many issues and it might not need all the pruning techniques.

Your seedling is most likely going to be one long shoot. You’re probably only going to be able to prune back to 1 or 2 leaf nodes …and well if you’ve only one shoot… that’s one cut and your done.  Fun over.

A whole year and all you’ve done is made 1 cut and now you are just left with a short stump. A twig sticking out of the pot …I told you it’s slow going. 

Years 1 to 2

There is not much going on during this year, but you may get the chance to do some work.


As the tree approaches its first birthday you may need to repot it, especially if you have been growing it in a small pot. The tree is probably going to have filled it with roots during the last year. 

However, If you’ve planted in the ground or in a larger pot. This is 50/50. I’d personally leave it and not repot for another year, but you could repot the tree at this point. The benefit of doing it now is that you can get in early and remove the tap root and start building your root structure. (Read my guide on – How To Remove The Tap Root)

However for a 1 year old tree, it’s not going to make much difference leaving it an extra year to get a little stronger and then doing this when its 2. The choice is yours. Maybe do half your seedling after a year and the other half after 2 years. Find what you personally prefer to do. 

Either way, repotting after 1 or 2 years, the goal is the same …Remove the tap root and start trying to get your radial root spread sorted out. You won’t have much roots, so don’t go to crazy, just do what you can while keeping enough roots to keep the tree alive. 

As for the top of the tree. I would just leave that to grow out all season untouched. Your little stump that you did at the end of its first year will hopefully explode with growth and push out a couple of branches


I would do exactly the same this year, leave it to grow and then in later winter prune it back. Again there will not be much work. I know I have had seedlings that split into two after my first pruning, meaning this time I had only 2 branches to cut back.

You tree is nearly 2 now and you’ve pruned twice, but only made 2 maybe 3 cuts. Give it a few more years and you will be pruning a lot more than this.

If you where trying to grow your tree large or get a thicker trunk, I might not even prune it at all, just let it get as big as you can for a few years before cutting it back.

Years 2 to 5

From year 2 to around 5 I would again just focus on letting the tree grow out.  It seems boring, but this is how you turn a seedling in to a bonsai.

I’ve heard different things, but roughly for every 1 meter a branch grows, it gives the base of that branch a thickness of 1 cm. So you can quickly see that you really need to let a tree grow a lot to get thickness.

I don’t know how accurate that is, but I know the longer a branch grows the thicker the base gets. This in turns fattens the trunk, which is what we are after. 

Between 2 and 5 years There are three general approaches you can take to pruning:

1. Building Structure and Thickness

I prune the tree back in late winter then repot in early spring. I then leave it untouched to grow freely until next winter. where I repeat the same procedure. This is generally now how I treat my of my seedlings.

This extremely slow and boring, but I am getting the best of both worlds. Its sort of balanced approach. The tree is allowed to grow as much as it wants, so there will be some thickness gained ,its not a but there is some.

However, I am also pruning it back once a year to make sure it is on track to start building some basic structure. Every time I cut it back in late winter it will usually divide in spring. This is how you go from 1 main shoot to 2, 4 and so on …But its slow, every year you will get one more divide, so it all adds up.

2. Building Structure

This approach is something I’ve done in the past and while it gives you some bonsai fun, you sacrifice the thickness of the trunk. After a few years you realise you have a great structure but your tree is pencil thin.

To do this you do as above, where you do the late winter pruning, spring repot. However, you only let the tree grow out until the end of spring before doing more prining.

The tree will have put on some good growth over spring and I will now and do the same techniques I used in winter. I cut everything back and Remove certain issues. There isn’t always a lot to do, but it’s still good fun. This causes the tree to push a second flush of growth, I then used to leave that to grow out for the rest of the season …although you could actually prune again in the summer and hope for a third flush of grouh

As I’ve removed any issues in late spring, the tree should hopefully spend its energy growing branches that are ones that i want and actually more useful over the long term, which means that and when winter comes there should be less issues to deal with.

As I already mentioned you will not really get any thickness doing this method, so much as its more fun, you have to be patient and avoid it for now.

3. Building Thickness

This is approach requires the most patience as you basically do nothing. You just leave the tree alone and let it grow.

You might repot it if required, but basically the top should be left alone. The idea is that the branches will get long and tall and the trunk will thicken a lot.

The plan is to then chop it right back and be left with a thick stump. From here you then start building the tree. You would start approach 2, where you focus on building structure. Its okay now that you will not get much trunk thickness, as you have already achieved that.

As much as approach 2 is more fun, if you can let your trunk develop thickness first you will end up with a much better looking tree.

I have a few tress I am doing this with. If I had more space I would be doing this with a lot more.


As for repotting, It doesn’t really matter what approach you take for pruning the top, your tree will just need repotted when it needs repotted.

I’m more inclined  to do a yearly repot, but this depends on the size of your pot and also the growth rate of your tree.

I tend to have fast growing trees in small pots, so my pots are full of roots after a year. If your tree is a little slower, or you have a bigger pot, you could get away with two years between repots. 

Obviously the more you repot, the more work you can do on the roots. But equally the more often you repot, the more you can potentially stress and weaken the tree. A good rule of thumb is, if the tree has grown really strong and healthy, it should be reported.

If your tree is in the ground. You can either leave it for a few years or again repot once a year. Just be careful. You don’t want to leave it too long and find the roots really over grown and out of control. 

(You can read more about – When Do You Need To Repot A Bonsai?)

The Timescale May Vary

I think its important to remember that not every tree will follow this time line exactly. While between 2 and 5 years is a good general guide for doing these techniques. You may find it takes longer or maybe even faster than this. 

If you are growing in the ground and want a small tree, you may find a year is long enough. If you want to grow your tree 3 inches across, but you are using a small pot, it may take 20 years? Who knows?

All I can say is that once you are happy with the thickness of the trunk and you can start seeing the direction that the tree wants to go in, you can begin to focus more on building the structure and styling the tree. 

This literally may be as simple as wiring one branch slightly down, which allows the tree to open up and give you the look you are after, or it may involve a little more work than that. 

Once you have a vision for where he tree is going, you can start to have more fun, it just takes a few years to get there from seed.

Years 5 To Ongoing 

Before now you will have only pruned the tree a few times through its life and its pretty boring, but usually around 5 years you should be able to start having more fun.

You goal really in these first couple of years is to get some decent trunk development and maybe a little bit of structure. If you dig a tree up from the wild or buy some nursery stock, you are basically skipping this first 5 years or so.

However, since you grew from seed, your tree has hopefully now started to develop and you will now want to begin focusing on ramification and really building out the structure. This is where the work really starts to build up and you will now be busy and actually feel like you are doing bonsai. 

This is also the point where you can usually dig your tree up from the ground or start taking it out of the large pot and trying to reduce the rootball down in size.

The Work Is The Same

You should still follow the same principle as you have every year so far. Prune back in late winter and repot in early spring if it needs it.

You will normally find as a tree gets older and you move from development to ramification, you will need to repot less often. It is also often beneficial for a tree to be slightly rootbound, as it slows the top growth, basically forcing it to have smaller growth, which is a part of ramification. 

The main difference between development and ramification is now you definitely need to be pruning back in late spring. You also depending on the growth, need to be pruning back in the summer as well. 

Basically you just keep on top of the new growth. Allowing it to grow out to about 6 or 8 pairs of leaves as an average guide and then cutting it back. 

Some trees grow faster than others, so you may find you can do this a couple of times in a season, maybe even monthly of the tree is going crazy. 

This contestant pruning will really build ramification and you will also find that the leaves get smaller and the branches get thinner. This is the stage when your trees really start to look like trees. This may take 10 years to happen, but this is when bonsai gets exciting and is worth the wait. 

You Still Need To let The Tree Grow

There is one important thing to consider at this time which is that you do need to let the tree grow. You cant just be pruning it constantly.

It is best to let it grow out to about 6 to 8 pairs of leaves. If you just see a new shoot pop and a week later you cut it, the tree would will get weaker and weaker. You will still be pruning often, but let it stretch out in between. The tree wants to grow, so let it. This is what gives it strength and vigor. 

Pruning branches when they reach 6 to 8 leaves is about ideal. If you just leave it fully unchecked and let it grow all year at this point, you will lose the ramification, the branches will thicken too much and all the fine branching will be lost. So you will have to cut back and start all over again. 

You will find tops of trees grow faster than lower down, so you may find you have to trim the top more often. It’s a bit of a balancing act.

You need to let the tree grow without it getting too much out of control, but making sure it’s healthy. You also don’t want the top to grow more than the bottom which will ruin the look of your tree. 

However, by this point you will have been caring for the tree for a few years as will have hopefully worked out how it grows and how it reacts, so you may be reading this while you have a seed germinating next to you and seen like daunting fact of trying to balance a tree is going to be too difficult, but do not worry over the time your tree grows you will learn how to deal with this easily. 

Don’t Get Overwhelmed

This might all seem liker a lot, but if you follow the development stage you will be more than prepared for the ramification stage. 

It’s a long a slow process so you will have plenty of time to learn and prepare. 

I would encourage you follow these steps. I know the urge to prune and wire is strong, but trying to style a 6 month old tree seedling is not the way to go.

Take your time and build the structure properly. Yes it’s slow and yes your tree looks crap for the first 5 years, but in 10 years you will have a tree so much better than you can imagine. 

Final Points

You will always find that bonsai haters are gonna hate. People are going to laugh and say your little tree seedling is rubbish and say it’s not a bonsai.

Well yes it probably is true, but you’ve got a 10 year plan and in 10 years you won’t have a seedling, you should have the start of tree with a good structure and ramification and it will be well on its way to being a bonsai.  

So, ignore the hate and keep growing your little tree. One day they will stop hating and end up being jealous of what you have created.