1. Prune Right After the Harvest

The best time to prune a citrus tree is immediately after harvesting the fruit. This is usually early spring or early fall, depending on the specific type of citrus and your growing zone. In most parts of the country, February through April are the best times to prune a citrus tree.

Citrus trees bloom and fruit on new growth so pruning right after the harvest gives the tree time to put on new growth. That new growth will protect the newly exposed wood from the summer sun.

Do not prune citrus between May and October since it exposes branches and trunks to direct sun, making them susceptible to sunscald.

2. Use the Right Tools

Use hand pruners to remove sprouts and small branches and a pruning saw or loppers on larger branches. Make sure your tool blades are sharp so your cuts are clean. And to help prevent the spread of plant diseases, sterilize your pruning tools by dipping them in a 10% bleach solution before you start pruning, and between separate trees.

3. Cut Branches Back to the Collar

When removing a branch from a citrus plant, cut it back to the swollen area where the branch joins the trunk. That area of plant tissue is called the branch collar, and it heals quickly after a cut is made. Making the cut just outside the branch collar also prevents weak sprout regrowth. If you make the common pruning mistake of cutting a branch off too high above the branch collar, the cut heals more slowly and there’s a greater chance that tree diseases or pests will attack.

4. Remove Dead and Damaged Branches

Remove large or small branches that are dead, damaged, broken, or diseased as soon as you spot them. One exception is if a citrus tree has been damaged in a freeze. In that case, don’t prune the afflicted branches right away. Sometimes new growth will emerge from the frost-damaged wood in the late spring. If there is no new growth by May, declare those freeze-damaged branches a lost cause and remove them.

5. Make Three-Part Cuts on Big Branches

When cutting branches more than 1 to 1.5 inches in diameter, use a three-part cut to ensure you don’t damage the tree. This precise process takes the branch off in 3 small cuts instead of one big one, reducing the chance of tearing the bark off the trunk.

• Make the first cut 6 to 12 inches from the branch collar. Starting from the underside of the branch, saw through 1/3 of the branch. This is called the undercut.
• 
  
• Make the second cut three inches farther out from the undercut. This time, cut from the top to the bottom until the branch falls away. If any bark starts to tear off, it will stop at the undercut.
• 
  
• For the third and final cut, remove the remaining branch stub close to the branch collar.
• 
  

6. Remove Suckers

Suckers, also known as water sprouts, grow from large branches or the trunk. They’re bright green without any bark. They tend to be thorny and unproductive and will make it hard to reach the fruit in the interior of the tree. Cut them off as soon as they appear to avoid having your citrus tree waste valuable energy on growing them.

Another place where suckers may pop up is below the bud union on the tree, where the citrus variety was grafted onto the rootstock. Rootstock sprouts tend to be thorny and produce inferior fruit. Snip them off as soon as they appear.

7. Cut Off Crisscrossing Branches

Remove branches that touch one another or the trunk. When the wind blows, crisscrossing branches can rub against each other, causing wounds that are entry points for diseases and pest infestations.

8. Remove Some Lower Branches

When left in their natural form, citrus trees are just overgrown shrubs. For the best crop, they should look a little scraggly; more leafy branches mean more fruit. However, it's important to remove some low-hanging branches so you won’t have fruit-laden branches lying on the ground.

That's not the only reason why you should prune some of the lower branches of your citrus tree. This type of pruning (skirting) improves airflow around and below the tree, which is key to preventing fungal diseases and pest infestations. It also helps with water distribution and makes it easier to access the tree to keep its base free of weeds, apply fertilizer, and harvest fruit.

9. Prune Lightly but Regularly

Doing light pruning every year is better than letting your citrus tree get overgrown and then doing a heavy pruning. Regular maintenance pruning will help your tree produce an annual crop, while heavy pruning may keep the tree from fruiting for one to two years.

An annual light pruning consists of thinning cuts to remove the 2 or 3 tallest, most upright branches on a tree each year. This improves airflow and lets more sunlight get into the canopy while keeping the tree compact and productive.

Never prune more than 15 to 20% of the canopy of a citrus tree in a year. The only exception is to remove dead wood caused by freeze damage.