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How to Prune Potted Citrus Trees

When I first got my potted Meyer lemon tree, I had no idea how to prune it or even knew that I needed to. But after finding out the benefits of pruning and with some practice, it’s almost a necessary skill when growing citrus trees. So, how do you prune citrus trees in pots?

You can prune potted citrus trees by identifying any dead, diseased, or overcrowded branches. From there, sterilize your pruning shears and make a clean cut close to the trunk. The goal with pruning should be to allow enough light and air in the canopy but still have enough healthy branches to grow and fruit.

While pruning can help citrus trees, do they really need it? If they do, when and how do you prune, and do you need to prune the roots at all? Let’s answer all of these questions.

Do Potted Citrus Trees Need Pruning?

pruning my potted Meyer lemon tree

Pruning potted citrus trees ensures new growth and healthy fruit while reducing the chances of the disease spreading or overcrowding the limbs. Pruning is essential to the health of the plant and also keeps the size and shape manageable while growing in a smaller space.

Pruning is the practice of cutting and removing branches and limbs from a tree. Typically, this is done after a harvest to ensure further growth.

Here are several reasons why you should prune a citrus tree:

  • Make access to the tree easier during harvesting and management
  • Allows for better light penetration through the canopy
  • Can increase fruit yield by focusing the tree’s nutrients
  • Allows for better air circulation
  • Will reduce fruit bruising by allowing more space from the limbs
  • Prevents overcrowding and over-fruiting

When pruning, first look for unhealthy limbs or ones that are stuck or poorly positioned. Too much pruning can damage or weaken the tree and affect fruit yield.

Although potted citrus trees do not need to be pruned to prevent overcrowding, they do require regular pruning to:

  • Encourage fruit production
  • Control the tree height (if kept indoors)
  • Remove dead or unhealthy limbs

Cutting individual healthy limbs is known as ‘applying controlled stress.’ This practice signals to the plant that it needs to create new growth and focus growth on existing buds. It is good practice to keep shoots short and slightly compact so that they can easily hold the fruit’s weight and so they can fit in the growth space.

How to Prune Your Potted Citrus Tree

To start pruning your potted citrus tree, take your disinfected pruning shears and cut any dead or excess branches. Remember to also remove the suckers or sprouts growing out of the base of the tree. Generally, pruning should be done in the early spring or after harvest.

If you keep your potted citrus tree outside, you may find that most of the pruning you’ll perform is cutting back unhealthy limbs to encourage new growth. For trees in an enclosed space, such as a greenhouse, it’s often necessary to prune to save space.

Gather Required Tools

Before you begin any pruning, it’s vital that you thoroughly sterilize your tools. Disease or unhealthy cells can spread from plant to plant if the tools are not properly cleaned between use. 

Since potted citrus trees are usually smaller than those found outside, most pruning can be done with a pair of shears. However, as the tree matures, it may require the use of loppers, which look like bolt cutters. The longer handles provide better leverage which makes cutting thicker branches much easier. 

It’s also possible to buy disinfectant designed for the cleaning of garden tools, but it is also easy enough to make your own solution:

  • Vinegar – vinegar is often an underrated cleaner. It’s very effective at disinfecting and doesn’t require any added chemicals. Since vinegar is made from fruit, it’s extremely environmentally friendly. I use a 50/50 water to vinegar spray as a multi-surface cleaner and shear disinfectant.
  • Isopropyl alcohol – with a 70-100% concentration, tools can either be wiped or sprayed with this solution to be immediately sanitized. 
  • Household cleaners – common cleaners found in the home, such as Lysol, can be used to clean gardening tools, though they are more expensive and harmful to plants and animals. Some can also be corrosive to tools and should be used only when diluted.

Aside from the cleaners, having a good pair of gardening gloves is recommended when using tools and handling larger plants and citrus trees. 

Assess What and Where to Trim

Before you make any cuts, take a thorough look at the whole tree to assess what and where pruning would be beneficial. Note any dead or unhealthy branches, any limbs that may have crossed over or look to be overcrowded. 

Look for Root Suckers

The first step is to look for root suckers. Chances are, your potted citrus tree was grafted from two separate trees. This is standard practice for most fruit-bearing trees. However, if you find small roots growing from beneath the graft line, they will overgrow and overpower the tree itself. These should be removed as early as possible and checked year-round. 

Find Unhealthy Limbs

If you find unhealthy looking branches or damaged limbs, cut at least six inches into the healthy wood. Otherwise, cut the branch just before it joins the rest of the tree. Always remember to thoroughly sanitize between cuts to prevent spreading any diseases that may have caused the issue. 

Remove Water Sprouts

Like root suckers, water sprouts grow at the base of the tree. But where root suckers tend to grow from beneath the ground level, water sprouts grow above ground from buds that haven’t sprouted. 

Although they don’t smother the tree, they grow tall, can crowd the fruit-bearing limbs, and should also be removed early. 

Prevent Overcrowding

Ideally, the canopy of the tree should allow for ample light to reach all the branches. With that in mind, cut back branches that may have crossed over or in areas that appear too thick. This should be done after harvesting before the next growth begins.

Similarly, trim any long branches just above the bud. Your tree will produce better fruit and have a better shape with shorter branches.

When pruning, take care to avoid thorns! To see which citrus trees have thorns, check out my other post here.

When Should You Prune?

For most climates, the ideal pruning time to prune potted citrus trees is February through April. However, in warmer temperatures, harvesting may occur earlier or later in the year. In general, the vast majority of pruning should be done after harvesting before any new growth begins.

On the other hand, pruning water shoots and root suckers should be done year-round. These are not fruit-bearing limbs and will not affect the harvest. Clip these growths when you see them to prevent them from growing too large. 

Do You Need to Prune the Citrus Tree’s Roots When Repotting?

Citrus trees never go fully dormant, meaning they should keep their leaves year-round. This makes repotting a challenge. However, root binding is a common issue with potted citrus trees, and repotting is necessary every 2-4 years.

Although citrus trees can thrive in containers, they will continue to grow, sucking all the soil’s nutrients and packing their roots into dense circles. This causes stress on the tree and can ultimately kill the plant.

In the video below by LogeesPlants, you can see how to identify root rot and what healthy roots should look like:

When it comes time to repot your citrus tree, follow these steps to successfully repot your tree and reduce the chance of transplant shock.

  1. Choose a time during which the growth of the citrus tree is at its lowest. This is often during the winter months, after harvest, and before new development. 
  2. Find a pot that’s the same size or slightly larger. Using a slightly larger pot will allow the roots to regrow into the new space. 
  3. Place some soil into the container. This will act as a base onto which your established plant will sit.
  4. Using your pruning shears, remove the roots that look to be the unhealthiest. Using the video above, you can see the difference between healthy roots and those that should be cut away.
  5. Repot in the new container and add soil up to 0.5-1 inch from the top rim
  6. Add a layer of fresh mulch to the top of the pot. Straw, leaves, or other organic materials make for a great mulch.
  7. Deeply water your newly potted tree.

Final Thoughts

When I first got my potted Meyer lemon tree, I didn’t know much about pruning. However, this article is everything I’ve learned about pruning to help your potted citrus tree remain healthy and bear a lot of fruit.

Remember, pruning your potted citrus tree should be done with sanitized tools after the fruit is harvested. Before the next growth cycle, cut back on unhealthy limbs or sections of the tree that may have become overgrown. Pruning in this way will encourage new growth and promote healthier fruit!