How to Prune Citrus Trees

how to prune citrus trees

Have you heard the old garden adage that you should prune your lemon tree so a bird can fly through it? Me too. I don’t know how these pearls of wisdom get ingrained in garden-lore but please don’t follow this one, not even for a little bird. I followed this piece of advice and killed a perfectly good tree as a result. Citrus trees don’t need, or like, a lot of pruning. Opening up a dense citrus tree too much just makes the tree work hard to produce new foliage and increases the chance of frost damage.

So how do you prune citrus?  Here is a quick guide to how what and when.

How to Thin Citrus Trees

Lemons, limes and bushy mandarin varieties like Clementine and Miho do benefit from some thinning. Oranges, Grapefruit and the satsuma varieties of mandarin do not benefit from regular pruning, but may require some renewal pruning every 10 years or so (see below).

For lemons, limes and bush mandarins, it is a good idea to do a bit of thinning each year after you harvest the fruit. Selectively trim back the fruiting twigs after you’ve picked. As you go along the branch, thin out a few shoots to keep the foliage open, remove any stems that overlap the trunk and vigorous water shoots.

how to prune citrus trees

You can also shorten branches, but always back to a lateral, (buds and branches).

how to prune lemons and limes

Removing Root stock Growth & Water Shoots

The photos below show the growth of shoots from the base of citrus trees. This is most common in young trees. These suckers or shoots that grow from the base can be either from the root stock or the main tree. Either way, it is a good idea to get rid of them. They are vigorous, more like water shoots, will not produce great fruit, take energy from the main tree and detract from the form you’re trying to establish.

Most citrus varieties are grafted onto a root stock called trifoliata, and more recently flying dragon root stock which produces a dwarf citrus tree. You will be able to identify the trifoliata suckers from the base because they will be coming from below the graft line and will have a distinctly different shaped leaf to the main tree and be quite spiny (see photo on the right below). They are more vigorous than the top growth and will take over the tree if left. You can rub these off as soon as you see them, anytime of year.

remove citrus rootstock growth

When to Prune Citrus Trees?

Winter is a good time to prune citrus because the dreaded citrus borer beetle is not on the wing. If you prune in summer when these little beasts are awake they will smell the citrus oil from the bark and fly on in for a chew. They bore holes into freshly exposed citrus wood and make themselves at home in the trunk, gradually killing the tree branch at a time.

Even when pruning citrus in winter you should still paint over exposed cuts with a pruning seal paste to seal the exposed wood. This also deters the boring beetles. If you live in a frosty climate you might want to wait until late winter when the worst of the winter has passed as pruning can expose foliage to the frosts.

If you do get frost damage on your citrus, leave it on until the new growth starts in spring. This way you can see where you need to prune back to as it takes a while for the damage to work it’s way down the branches. The frost damaged foliage also protects the rest of the tree.

How to Renew Old Citrus Trees

Citrus are long lived and some of them can get to be quite large. My sister has a meyer lemon at her place that must be at least 30 years old and is taller than the garage. Tackling a pruning job like this can be a bit daunting and risky.   If you remove too much of the canopy in one hit you risk killing the tree. The best approach is to do it in stages over 2 or 3 winters to let the tree recover and put up new growth.

Your goal with a big old citrus tree is often to reduce the overall size of the tree to make harvesting easier and promote the growth of new fruiting wood. The method is to cut back branches to within 1m of the main trunk (see photos below for how to do this).  Always cut the branch to a junction with a lateral as new growth will only come from buds near the cut. Cutting off branches nowhere near a lateral results in a bad haircut and no new growth or fruit. When you’re pruning, look at the overall shape as well as what you are cutting back to.   A bowl cut may be the shape you’re after, but if you’re not pruning back to a lateral, the tree won’t put on new growth quickly, and your cuts will look like ugly stubs with no leaves.

When you do it right, the new growth after this kind of heavy pruning is often pretty dense, so it is a good idea to make a second pass with the secateurs when this growth starts and thin out the new branches a bit. This will give you bigger fruit too.

After heavy pruning it may take a couple of years for the tree to start cropping well again. If you are going to renew old citrus trees then pruning alone will not do the job. You need to combine pruning with a good fertiliser and pest control program for a couple of seasons to bring the tree back up to full health.

How to Remove a Whole Branch

If you have a borer infestation in a side branch, or need to remove a whole branch as part of a renewal program for an old tree, then the photos below show how to cut it off properly. With a sharp pruning saw make a few strokes underneath the branch to break the bark.   This will stop the bark ripping when the branch comes off.  Ripped bark doesn’t heal cleanly and can let in fungal diseases and insects.

Cut the branch off close to the trunk, leaving enough branch for the tree to heal the wound around the cut. If you leave too much branch you will get a stub that dies off and rots, rather than a clean heal. Likewise, if you cut too close to the trunk it won’t heal, leading to infection and rot in the tree.

how to prune a lemon tree

PS. the “ground pruning” photo at the start of this post was actually a big old mandarin tree that didn’t agree with my approach to citrus pruning.



  1. I have a wonderful Mandarin tree that I planted 30 years ago. I have never pruned except to remove dead parts. New growth comes at the ends of last years growth, making the branches longer and longer. This year there is plenty of fruit but it is small and the loss of leaves is concerning. Will pruning the ever longer branches rejuvenate the tree? If so, where should I cut?

    1. Hi Jim, yes it will but don’t go too hard on it. Do 1/3 of the tree each year until it is all pruned. Don’t take too much off, just thin and shorten. Always cut back to a join in the branch – see the blog for photos. Thin the fruit when young for larger fruit.

  2. Hello,

    Is there a good reason to prune my tree? I have a lemon tree that is about 10 years old, in San Diego, CA, and I have never pruned it. Lemons are on the tree year around. Is that a problem? Should I prune the tree? I try to take off the rotten ones, otherwise they just fall off. I’ve looked on the internet for answers and nobody has an answer for me. In colder areas there are rules for taking care of a tree because of freezing. PLEASE HELP!

    1. Hi Kim, no there is not. If it is doing well don’t prune it. The reason to prune a citrus tree is to reduce its size or thin out foliage that is getting too dense. The more important thing to do is harvest the fruit like you are doing. Leaving old fruit on the tree draws resources away from production of new fruit. If you start getting fungal disease or lots of pests on leaves like little white fly then the time might be to thin it out a bit. Otherwise hands off is fine.

  3. I agree if you prune your citrus trees in the winter or as it gets colder I have seen better results. Great article, I love to read about how to take care of trees and this was interesting not boring like some of the stuff I read. Thanks for that.

    1. You’re welcome Bob, glad you’ve had good results with winter pruning too.

  4. I have citrus that were neglected and the rootstock has grown taller than the scion. The lower branches carry the edible fruits and the tallest ones a very bitter fruit. I am afraid it will overtake the scion. Can I safely prune the rootstock even though it is bigger than the parts with tasty fruits or will it kill the whole tree?

    1. Hi Ariel, yes get in there and remove the rootstock. Maybe do it over two seasons to lessen the shock to the tree. Half this year, half next and give the tree a good feed with citrus fert to help the proper growth recover.

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