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How To Prune A Lemon Tree

Pruning lemon trees is essential for keeping them growing and productive, but the timing, methods, and reasons for pruning your lemon tree are very different from the timing, methods, and reasons for pruning stone fruit trees like peaches, cherries, apricots, plums, and nectarines or pome fruit trees like apples and pears.

There are also different times, reasons, and methods for pruning depending on whether the lemon tree is indoors or outdoors. Pruning lemon trees can be fun; it’s a sign of good things to come. Let’s dig in!

How to Prune a Lemon Tree
Hard pruning for neglected citrus trees.

Lemon trees can grow really big. Depending on the variety, an unpruned lemon tree can and will grow 30-40 feet tall and 30-40 feet wide if it has the right growing conditions.

We’ll divide this article on how to prune a lemon tree for the best health and the best structure while keeping it contained into two sections. We will start with everything you need to know about how to prune a container-grown lemon tree, and then we will discuss how to prune an outdoor lemon tree.

How to Prune a Lemon Tree Grown in a Container

Potted Lemon Tree
Lemon tree in terracotta container.

Unless you are a home gardener living in an exceptionally mild and arid climate (USDA Hardiness Zones 10 through 13,) chances are that you grow your lemon trees in containers that you take indoors in the winter.

If you have had your lemon tree growing in a container for three years or more, you probably have some branches that look like dead wood even though they have some healthy leaves on the end. Dead wood is a sign you need to do some pruning, but it is also a sign you have been doing a lot of things right.

Lemons are fussy feeders. They like to have their roots moist, but not damp. If you have followed all our instructions on how to grow a lemon tree, you have given them a container that is small enough to keep their roots from getting soggy, preferably a clay pot, but big enough to support growth to about 4 feet tall.

Unless you plan to nickname your lemon tree Godzilla (the writer of this article has a friend who let his indoor lemon tree get 25 feet tall), you need to stop dead wood by topping your tree.

When you have branches that have living buds on them but don’t leaf out until you reach the end, it’s as if your lemon tree is telling you, “If you would just put me in a pot big enough for me to grow 25 feet tall, I could safely put out some leaves there.” But if you want to keep your lemon tree manageable, you need to top it so it’s no more than 4 to 5 feet tall.

The horticultural term for this condition is tip dieback, or flagging. Both terms mean the same thing. When a tree of any kind has more growth on top than its roots can support, flagging can set in.

Root stress in a container-grown lemon tree doesn’t always cause flagging.

Sometimes a lemon tree doesn’t have dead wood, but it doesn’t give you any lemons. This can also be a sign you need to top your tree. If you let your lemon tree grow too tall in its container, it may have just enough energy for foliage but not enough energy for fruit.

How to Top a Container-Grown Lemon Tree

Topping a lemon tree is something you do branch by branch. You don’t just take electric hedge trimmers and whack off its top.

Look at the branches at the top of your lemon tree. Look for branches that have new growth on their tips, but are missing leaves between the free end of the branch and where it attaches to the trunk.

Lemon tree in container

Maybe you will see spots on the branch where young leaves fell off. The branch may still be green, but it drops all the leaves. If you notice healthy leaves that seem to be getting smaller at the end of a branch that is missing leaves, or you have a green branch with no leaves, or an older branch that looks dead, you have a branch that is flagging.

Don’t leave a green branch that just has one leaf at its end, either. A green branch that has lost most of its leaves is also a flagging branch.

You will find most flagging branches at the top of your tree, or as high as your lemon tree has the root resources to grow. Remove flagging branches one by one to reduce the height of your tree.

If you have a lemon tree that is 5 to 6 feet tall in its pot, you will usually need to remove about 25% of its branches. But don’t remove any branches that are green and filled in with leaves all the way back to their stem unless your tree is growing too big for the room where you keep it.

And don’t remove branches with flowers! Flowers are a new fruiting zone. But any areas of barky wood should be examined for removal.

Remove Inedible Fruit

Fruit production takes a lot of energy from your lemon tree. There is no point in keeping fruit you won’t be able to use on the tree.

This problem usually occurs when people leave their trees unattended for weeks on end. The lemon tree might have young fruit on it when they leave, but they come back and find split or withering or brown fruit.

Lemon tree

As long as the fruit are on the tree, they take resources from edible fruit. Removing fruit you will never harvest redirects energy to fruit you will use. Remove any flagging branches bearing inedible fruit, too.

If inedible fruit is a problem on your tree even when you are watering and feeding it properly (see our article on How to Grow a Lemon Tree for general instructions), what you need to prevent the problem may be feeding your tree micronutrients after it blooms. Or if your lemon tree blooms all year, you may need to give it supplemental micronutrients all year long.

Here are some of the nutrients required for proper lemon tree growth:

  • Boron is essential for the lemon flower to make the tiny tube that receives the pollen that sets the fruit.
  • Boron, zinc, and calcium power pollen production. Lemon trees that don’t get enough of these nutrients aren’t self-fertile. This means that one lemon tree isn’t enough when its soil and fertilizer are deficient in these elements.
  • Boron and molybdenum are necessary for the lemon fruit to make the sugars it needs. Even though lemons are sour, they contain small amounts of sugar that give them the energy to grow.
  • Calcium helps lemon fruit resist mildew and mold.
  • Copper is an essential element for the enzymes the lemon fruit makes to use sugars to grow.
  • Iron is a cofactor for chlorophyll that keeps lemon tree leaves green.
  • Magnesium is in the middle of the chlorophyll molecule.
  • Silica helps fruit, leaves, stems, and roots take up both macronutrients (nitrogen, phosphorus, and potassium) and the previously-mentioned micronutrients (boron, magnesium, calcium, molybdenum, and zinc) more efficiently.
  • Sulfur is essential for the plant’s production of two amino acids in the lemon fruit, cysteine and methionine. Cysteine is a building block of every organism’s DNA, and methionine is essential for the production of ethylene, which helps the lemon turn yellow.

Sometimes your lemon tree will need both micronutrients and pruning of branches with inedible fruit. But if you give your tree needed trace elements, you won’t have to prune inedible fruit as often.

To recap, there are two things to remember about removing inedible fruit:

  1. Don’t remove branches with flowers! Flowers are a new fruiting zone. But do remove nearby inedible fruit to prevent the spread of mold and bacterial diseases.
  2. Remove excessive fruit. Lemon trees can fruit themselves to death. Removing inedible fruit at the first sign it is going bad may save your tree.

Pruning a Grafted Tree

Many lemon trees sold for container growing are grafted. The grower chooses a rootstock, usually a bitter orange, to keep the tree small and to help it withstand drought and chilling.

The grower clones a productive, mature lemon tree by attaching a scion from the lemon tree to the rootstock of (usually) a bitter orange. The result is a tree that is happier growing in a container and more resistant to problem growing conditions.

Sometimes the rootstock will send up suckers from the rootstock. If the rootstock spouts, you are essentially growing two trees in one pot. The second tree won’t produce edible fruit. You need to remove any top growth from the rootstock.

Suckers from the rootstock poke through the soil around the main trunk. Remove them whenever you see them!

How to Prune a Lemon Tree Grown Outdoors

Lemon Trees in an orchard
Lemon trees in local orchand

If you live in a climate where lemon trees grow outdoors, there will eventually be a time that your tree grows above ground as its roots can support.

Maybe your soil has a hardpan a few feet down, or maybe the roots of your tree hit rock or concrete a few feet away from the trunk. There will be a point at which your tree can only support so many branches, so many leaves, and so much fruit on the soil and water available to its roots, so you have to prune it.

When Do You Prune Outdoor Lemon Trees?

The first question everybody asks about pruning outdoor lemon trees is “When?” The best time to prune a lemon tree growing outdoors is right after you have harvested your main crop of the year, or just before it goes into heavy flowering.

Some outdoor lemon trees will flower and bear fruit all year round, but most lemon trees will bear one or two heavier crops annually. Prune just before heavy flowering or just after a heavy harvest.

When your lemon tree has dead wood, however, the time to prune is now. You always want to remove dead wood from your outdoor lemon tree. Even if there are a few leaves on a woody branch, it should be removed.

Start Pruning from the Top Down

As lemon trees reach the limits of their resources, they have more and more trouble sending water and nutrients to the top of the tree. You will find the most branches with dead or nearly-dead branches at the top of the tree.

Look for places in the canopy where you can see light, and identify flagging branches (described earlier in this article). Remove each branch at the main stem.

This is where pruning a lemon tree is different from pruning an apple tree or a stone fruit tree, like peaches, cherries, nectarines, or plums. When you are pruning an outdoor lemon tree, you want to remove branches flush with the stem from which they are growing. Pruning cuts are important when pruning a lemon tree. Cut as close as you can to the branch. There should be no stubs.

Don’t leave any dead or flagging wood on a stem. Make the cut as flat as possible. You want your lemon tree to heal with the wound by growing bark over the previous stem bud so that branch won’t ever try to grow back. This keeps your tree from producing more flagging branches.

Sometimes You Prune Just to Keep Your Tree From Getting Out of Control

It’s especially easy to recognize healthy growth on vigorous Eureka lemons. Healthy new foliage will have a purplish, brownish tinge that matures to dark green after the Eureka tree flowers and sets fruit.

Sometimes you will want to remove even healthy growth. A Eureka lemon that has been grafted onto dwarfing rootstock is typically 3 feet tall when new. In just two years of good conditions, even on a dwarfing rootstock, it can easily grow 12 feet (almost 4 meters) tall.

Healthy Lemons on a pruned lemon tree

Letting your lemon tree grow 12 or more feet tall defeats the purpose of grafting it onto dwarfing rootstock. Keep smaller lemon trees to the size you want by pruning them lightly all year round.

To prune an outdoor lemon tree to keep it from growing too tall, make your cut at an angle on a branch at the height you want just above two healthy leaves.

Paint When You Prune

Every time you prune your outdoor lemon tree, you should give its lower trunk a coating of protective paint. Lemon trees can get sunburn. Tree guard paint protects the trunk against sunburn, insects, and rodents. 

Paint the lower trunk of your lemon tree at least once a year but no more than twice a year. Lemon tree trunks that aren’t protected from the sun will crack and become susceptible to boring insects.

When you prune the top of your tree to keep it healthy, letting more sunlight through, you need to paint the bottom of your lemon tree to keep it healthy, too.

One More Pruning Tip

If you can’t bear to prune healthy growth but you don’t want to let your lemon tree grow too tall, consider shaping it so it grows out rather than up.

Tie small bottles of water to the branches so your tree grows outward. Eureka lemons are especially amenable to this technique since they put out vigorous growth that reaches for the sky.

Now that you’ve learned how to prune a lemon tree, to learn more about how to properly grow and care for lemon trees, visit our Lemons page. You’ll find all sorts of resources for keeping your tree healthy, plus blog posts about different lemons you can grow and ways to use the fruit in your kitchen.

Ready for more lemon content? Next, visit our lemon trees page to discover more useful and fun information on lemon planting, growing, harvesting, cooking, and more!

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Monday 6th of March 2023

When should you transfer a lemon tree that is started to bear fruit?


Saturday 11th of March 2023

Not sure what you mean by transfer? Is it in a pot and you want to plant it in the ground?

Nic Keiderling

Saturday 2nd of July 2022

Can you tell me what causes many lemons on my tree to grow to the size of large grapefruits?


Monday 4th of July 2022

Ha! Not really... what variety is it? Where are you?


Tuesday 7th of June 2022

Hello I would like to know if a standard grafted eureka lemon tree could be maintained at 6 ft tall? I need to keep that height because I need to keep it in a cage for bird protection.


Friday 10th of June 2022

If it's a dwarf tree, then maybe. I'm not sure what you mean by "standard grafted". "Standard" generally means full-size tree. Grafted implies it was put on different rootstock - usually to dwarf the tree.

Michael Clement

Sunday 24th of April 2022

Nice explanation. I would like to hear more on orange trees too.

Deboragh Wigmore

Friday 3rd of December 2021

Great instructions and informative information on how to look after lemon trees


Saturday 29th of January 2022

Thanks Deboragh!