How to prune a lemon tree

It’s important to know how to prune a lemon tree if you want a healthy plant abundant with zesty fruit.

Lemon trees are a popular addition to patios, and make delightful house plants in conservatories and sunny living rooms, and give a Mediterranean flavor to kitchen garden ideas. 

A slow-growing fruit, lemons can take up to a year to go from bud to edible fruit. So patience is key – invest some time pruning your lemon tree now, and you will lay the foundation for a bountiful crop later on.

Whether you have grown lemon from seed or bought it from a garden center, it’s essential that you don’t neglect it and allow it to become overgrown and unproductive.

How to prune a lemon tree – step by step guide

Lemon trees should be pruned from their second year onwards, otherwise they can become very leggy, overcrowded with branches, and out of shape.

First, make sure you have the right tools for the job. ‘The most important part of pruning a lemon tree is to use very sharp pruners that have been disinfected with rubbing alcohol beforehand,’ says Joseph Marini, principal of At Home with Joseph (opens in new tab). 

'Cuts that cause tears can introduce disease or stress, and pruners that have been previously used on diseased plants can cause cross contamination to your lemon tree.’

However, for branches you may need a more substantial tool. 'Typically your lemon tree will be better served with a clean, sharp hand-saw or pole-saw (for higher branches), which will make much more precise, and neat incisions,’ advises Andrew Gaumond horticulturist, botanist, and director of content at Petal Republic (opens in new tab).

1. ‘To start with, remove suckers or basal shoots at the base of the lemon tree,’ says Marini. Suckers are very fast growing and often their leaves look different from the grafted part of the tree. If you don’t remove them flush at the base, they will steal water and nutrients from the rest of the tree, so do this as soon as you notice them.
2. Next, remove any dead, diseased or damaged branches. ‘Any growth that appears discolored, diseased or has been invaded by any pesky insects (such as scale or mealy bugs) should be removed immediately as and when they appear throughout the year,’ adds Marini.
3. Thin out branch structures. ‘Over time lemon tree branches will often start to compete with one another for light and nutrient sources,’ says Gaumond. ‘Thin out overlapping branches, and the overall structure of the tree so it has sufficient aeration and access to light. More mature branches shouldn't be cut flush to the trunk or parent branch – instead, leave at least 5 inches of branch in place, which will better enable the tree to recover from the shock of pruning.’
4. ‘Where there are double shoots that run almost parallel upwards, cut off the inside shoot,’ advises Sigrid Hansen-Catania, author of Success with Citrus Fruit (opens in new tab).
5. Hansen-Catania also recommends removing shoots that grow horizontally into the crown (cross shoots), making it denser, as well as any weak shoots that hang downwards – these should be cut off at the base.
6. When pruning a lemon tree, it’s important to think about the shape. ‘A citrus plant is particularly attractive with a shaped crown, and the round crown is characteristic. ‘To do this, target the left side and cut off selected shoots,’ says Hansen-Catania. ‘Do not take any notice of flowers or fruits. The point where you cut should always lie above a leaf.’
7. Finally, be careful not to cut off too much. ‘Never prune more than a third of a tree in one year,’ says Marini. 

When should lemon trees be pruned?

Ideally prune lemon trees in late winter or early spring. ‘The trick with all citrus trees is to avoid pruning or cutting back during the flowering and fruit producing season in summer when the tree is at its most virile,’ says Gaumond.

‘Citrus trees will enter a natural period of dormancy post harvest – typically late fall through winter – which is the best time to consider pruning. Typically, I'll assess a lemon tree in the very early spring to assess what needs pruning before the growth cycle reboots for the season.’

Pruning potted lemon trees

Potted lemon trees should be pruned in exactly the same way as other lemon trees, but you should be conscious of keeping them to a manageable size. 

'Although you can prune the branches to achieve the needed size of the lemon tree, it’s not enough. Lemon trees can grow up to 20-25 feet, but you don’t want them to do that inside your house,’ says experienced botanist Ronnie Collins, who also founded Electro Garden Tools (opens in new tab). 

‘Make sure to stop providing the plant with larger pots as soon as it reaches four feet tall. It’s an optimal size for fruiting in a pot. A pot of the right size will prevent the plant from growing larger.’

Hard pruning citrus trees

Occasionally lemon trees need a hard prune to rejuvenate them. ‘A radical cutting back is the last-ditch means of healing a citrus plant,' says Hansen-Catania.

'A lemon tree, for example, that has been overwintered in a room that was not sufficiently bright and too warm will react to these unfavourable conditions with increased loss of leaves. Cutting back will then be the only way to renew the plant and help it to grow healthy shoots. 

'Cut the plant back by about half and at the same time try to bring the crown into shape. The best time to do this is in the spring, before a new growth spurt begins.'

Can you over prune a lemon tree?

It is possible to over prune a lemon tree, which will impact its fruit production, and potentially kill it. Don’t cut it back by more than a third unless you are attempting to renovate a failing plant, in which case you can cut it back by up to half its current size.

How do you prune a Meyer lemon tree?

A Meyer lemon tree is a hybrid variety from China that is a cross between a lemon and a mandarin. It produces smaller, smoother, sweeter fruit with a thinner skin. You can prune Meyer lemon trees in the same way as other varieties.

Should I cut the thorns off a lemon tree?

Many lemon varieties are bred not to have thorns, especially grafted varieties, so check to see whether the thorny branch is in fact a sucker. This will be growing from the rootstock below the graft. If so, remove it.

If you have a thornier lemon tree variety, you can remove the odd inconveniently located thorn without risk of harming the plant. However, there is no benefit to removing all of them, and you may cause damage to the plant by doing so.

Can you top a lemon tree?

You should not cut the top off a lemon tree and expect it to survive. If the plant requires a hard prune to renovate it, you should cut the branches by no more than half.