How to Prune a Lemon Tree the Right Way

When considering how to prune a lemon tree, keep in mind that: “Pruning is generally not required to keep citrus productive or attractive,” according to UC Davis. “However, you should remove deadwood, very weak shoots or suckers and prune any crossing branches.” California Rare Fruit Growers calls those discards the four Ds: “dead, damaged, diseased, and dysfunctional branches.”

Just don’t get carried away with your cutting. “Excessive pruning usually results in reduced fruit production, vertical shoots called water sprouts, and suckers,” warns Alabama A & M Extension.  Therefore, never remove more than 20 to 30 percent of your tree’s canopy.

Project Overview

Working Time: 30 minutes
Total Time: 40 minutes
Skill Level: Beginner
Estimated Cost: $30 to $90

When to Prune Lemon Trees

Since lemon trees can bloom and bear on and off throughout the year, it may be difficult to prune them without also removing flowers and fruit. However, they generally bloom most heavily in late winter and spring, and then fruit most heavily in fall.  

Therefore, Laurelynn and Byron Martin advise in their book Growing Tasty Tropical Plants: “For the least disruption to fruiting, wait until the spring flush of flowering is complete to head back plants.” Spring’s new growth also will allow you to easily see which branches were winter-killed and should be removed.

Before You Begin

If you’ve used your pruning tools on other trees, soak them in a bleach solution—one part bleach to nine parts of water—for 10 minutes before you begin cutting. That will help prevent the spread of disease. Also, wear long, heavy gloves to protect yourself from lemon tree spines.

STEP 1: Remove any suckers and water sprouts from your lemon tree.

Except for seedlings, most lemon trees are grafted onto more vigorous rootstock such as trifoliate orange. Suckers are the vertical shoots which sometimes emerge below the graft from that rootstock. They should be removed at once since they “suck” energy from the actual lemon tree and produce inferior fruit.

Water sprouts do the same, but spring from dormant buds on the tree branches instead. Cut both suckers and water sprouts back to the trunk, root, or branch from which they emerged. Use pruning shears for shoots under ½ inch in diameter, and use loppers or a pruning saw for larger ones. 

STEP 2: Remove branches which are dead and those marked by disease.

Avoid tip pruning lemon trees since that causes heavy growth where the cut was made. Instead, if part of a branch is dead or diseased, remove the entire branch.

To avoid causing a large one—more than 1 inch in diameter—to tear away from the trunk when you are cutting it, use a pruning saw to make your first cut part way up from the bottom of the branch at a 1-foot distance from the trunk. Make your second downward cut a little further out. Then saw the remaining 1-foot stub off closer to the trunk, leaving its “collar” in place. 

STEP 3: Remove spindly branches and those which cross into the center.

According to IFAS Extension “Three to five main shoots should be selected at planting to form the primary scaffold framework for the mature tree.” Thereafter try to keep the center of the tree open enough that dappled sunlight falls on the ground beneath it at noon.

You can do that by removing spindly branches and those which cross into the center of the tree from the outside. Also, if two branches are rubbing against each other, remove the smaller one. You may snip off lemon tree thorns too, if you prefer, to prevent them from scratching you.

Pro tip: If you remove enough lemon tree leaves that the branches are exposed to direct sunlight, you’ll need to whitewash them to prevent burning from the sunlight. To whitewash, mix one part of white interior latex paint with one part of water and brush it onto the exposed branches. That should provide sufficient sunscreen to allow your lemon tree to bask rather than bake.

STEP 4: Thin the lemon tree back to the height you prefer.

If you are growing lemon trees indoors, it’s likely that you’ll want to keep them no taller than 5 feet or so. However, a dwarf lemon tree that doesn’t surpass 10 feet also is a good idea for outdoors, so you can harvest fruit while standing on the ground.

When cutting back lemon trees, avoid shearing off the tips of these fast-growing fruit trees as if they were hedges—unless they actually are hedges. Instead, shorten each too-tall shoot by pruning it back to the next lateral branch. Because lemon fruits bend branches, keep the lowest ones at least 2 feet above the ground.

STEP 5: Root prune a container tree to keep it small enough.

An important part of how to trim a lemon tree is how to trim its roots. If your potted specimen is outgrowing its container but you don’t have room for a larger one, lemon tree care may require you to prune its underpinnings.

Remove your recently watered tree from its pot and use a sharp knife to slice off 1 to 2 inches of the roots and soil around the outer edge of the root ball. After returning the tree to its container, add fresh potting soil to the space now opened up between the root ball and the pot.

Final Thoughts

Whether your lemon is an indoor fruit tree—which you grow as a big houseplant—or a larger outdoor cultivar, the above directions on how to prune citrus trees should help you keep it growing and glowing.