This is part 6 of a 7-part series of how to grow fruit trees easily.

I commonly get questions from readers about pruning. What to prune, when, how, and even why. Fortunately, we get a lot of pruning practice from managing our fruit trees. So, I put together this guide to help break down the different steps. Here’s a quick summary:

Before you prune, make sure your pruning shears are clean (wipe with vinegar or alcohol). Next, select branches that are dead, diseased, or overlapping. Generally, you want to increase the load-bearing capacity to support its fruiting and trim any branches close to the soil. Make 45º cuts and prune in the late winter.

Let’s take a look at all 10 tips in more detail.

By the way, these are the pruning shears I use and recommend for fruit trees.

Tyler pruning his nectarine tree
Tyler pruning his nectarine tree

1. Use Clean Pruning Shears

pruning my potted Meyer lemon tree

Getting the obvious tip out of the way, clean your pruning shears before you start making cuts.

When you cut a branch, you’re cutting through the bark, which naturally protects the tree from pests and diseases. So, by pruning, you’re essentially causing a wound and exposing the tree’s immune system.

Cleaning pruning shears is even more important if you’re dealing with diseased fruit trees. With dirty pruning shears, bacteria or spores from the disease can easily be carried from one tree or even one branch to another, on the same tree.

Because of this, it’s recommended to clean your shears after each cut.

However, if you’re not working with diseased fruit trees, you should be okay cleaning the shears between every tree.

2. Prune in the Late Winter

There are 3 key reasons to prune in the late winter. It’s a balance of:

  • Dormant Pests & Diseases
  • Sufficient Time to Heal
  • Enough Energy to Survive Winter

Since pruning exposes the immune system of trees to pests and diseases, the best time to prune them is when these threats are dormant—in the winter. Pruning in the winter gives your tree enough time to heal and close the bark before the pests and diseases are active again in the spring.

But you don’t want to prune too early in the winter.

Fruit trees also need energy to survive the winter, and pruning weakens them. So, prune in the late winter, or more specifically after your last frost.

However, if you live in a place that doesn’t get a winter (like I did in Florida, California, and Texas), then you can prune more freely. I would still recommend pruning before the growing season, so the tree’s new growth doesn’t go to waste.

3. Cut at a 45 Degree Angle

Tyler pointing to where to prune a fruit tree branch
Cut before the node. Sometimes that’s halfway up a branch, and other times it’s next to the trunk.

When you’re ready to prune, cut at a 45º angle. This helps water drip off the branch, preventing issues such as mold or disease from entering the tree’s cells.

Some gardeners even use grafting tape or wax to keep pests and diseases out of the wounds. While these methods are helpful, they’re not always necessary. However, feel free to incorporate them into your pruning routine to help your tree heal quicker.

Now that we know how and when to prune, let’s take a look a which branches to cut.

4. Prune Branches Close to The Ground

Tyler showing which fruit tree branches to prune close to the ground

The first thing I look for when pruning fruit trees is any branches that are close to the ground.

The primary issue with low branches is that fungal diseases often begin in the soil. During rain or watering, these spores splash up from leaf to leaf, quickly contaminating your whole fruit tree. Keeping your fruit tree’s branches off of the ground dramatically prevents these spores from spreading.

For adolescent or mature fruit trees, I recommend pruning branches at least 2-3 feet from the ground. Depending on the size of the tree, this figure can change, so use your best judgment for what looks natural.

In the wild, browsing herbivores would eat branches within reach—naturally pruning them. However, since our backyards often lack these animals now, it’s up to us to manage and trim our fruit tree’s canopy.

5. Prune Dead or Diseased Branches

Tyler pruning a dead branch on his nectarine tree

Along the same lines, the next thing I check for are any dead or diseased branches.

Dead branches are a risk for fruit trees as they’re a drain on nutrients and allow pests and diseases easy access inside the fruit tree.

Diseased branches are of course a risk as the fruit tree is actively trying to fight the disease, expending energy on them. They also continue to spread to other branches.

I suggest removing both of these types of branches, cutting them at a 45º angle, and fully removing the dead or diseased section.

While the diseased branches can be composted, many gardeners suggest burning them to prevent any further spread of the spores or bacteria. Dead branches can simply be composted (they’re great to use in Hugelkultur).

6. Prune Overlapping Branches

Tyler showing two branches on his fruit tree
These two branches are overlapping. I pruned the lower one as it’s growing towards the ground.

Other things I look for when pruning fruit trees are any crossing or overlapping branches. These branches often impede the growth of other branches and cause future issues such as crowding and lack of airflow (increasing the likelihood of mold and disease).

At the same time, look for branches that can support the future weight of the tree (and its fruit). When mature, fruit trees can have several hundred fruits, significantly weighing down the tree and putting stress on the branches. If any are at odd angles, they can snap at the weak points.

If I remember correctly from my 6th grade engineering class, a triangle is one of the strongest shapes. So, we’d want our fruit trees to roughly look like an upside-down triangle—with all of the branches being properly supported by the trunk. Otherwise, we risk the branches or even the trunk snapping.

7. Prune Branches That Extend Past The Canopy

Tyler showing where to cut the excess canopy on his fruit tree

One of the last things I look for is any branches that grow beyond the normal range of the tree’s canopy. There will be times when a branch of your fruit tree has access to more sunlight or nutrients and will shoot out faster than the rest of the tree.

Similar to the above, to prevent future issues with load-bearing, prune these branches to shape the canopy into a nice crown.

8. Leave 1 Leading Stem to Become The Trunk

Tyler showing the top two branches to prune
Our nectarine tree has two main terminal branches. I chose to keep the one on the right because it’s growing straighter.

If your fruit tree has not yet reached a mature height, it’s best to train one stem to become a continuation of the trunk. This supports the best load-bearing of the tree as three primary branches can stress the trunk, pulling it in multiple directions.

To do this, look at the natural shape of your tree and the angles of the branches. Which one do you see becoming the trunk of the tree? Which ones look like they’ll grow at an awkward angle, potentially posing a problem for the tree in the future?

9. Prune Flowers & Fruit On Young Fruit Trees

This is more of a growth tip, but if you have a young fruit tree (generally under 3 years), it can grow significantly faster if you prune any flowers or fruit off the tree.

I know what you’re going to say. “What’s the point of growing a fruit tree if you’re cutting all of the fruit off!?“(This is a real response I got from my mom).

But if you want your fruit tree to grow and fruit faster, cutting off the early flowers and fruit makes sense. Flowers and fruit take significant nutrients and energy (as does most reproduction in life). So, pruning these redirects the energy to the fruit tree’s root system and canopy.

Then, when your fruit tree is mature, you can stop pruning the flowers and fruits and enjoy them. Speaking of…

10. Prune Excess Canopy on Mature Fruit Trees

Just like how young fruit trees benefit from pruning flowers and fruit, mature fruit trees benefit from pruning excess canopy growth.

Instead of supporting unnecessary branches and leaves, your fruit tree can have its nutrients redirected, increasing its flowering and fruiting. If done properly, it’s able to support and produce more yields.

It’s not uncommon for mature fruit trees to produce several hundred fruits in a single season. We didn’t count, but I estimate our mature lemon tree gave us over 300 lemons this past season.

Bonus Tip: Pruning Makes Trees Immortal (Kind Of)

Our nectarine tree after pruning

Pruning, along with pollarding and coppicing (fancy terms for cutting a tree down to its trunk), is said to reset the tree’s lifespan by promoting new growth. This new growth ages differently than the rest of the tree.

“Trees being coppiced do not die of old age as coppicing maintains the tree at a juvenile stage, allowing them to reach immense ages.”


So, by pruning your fruit tree, you’re essentially helping it stay immortal.

Of course, the tree will still be vulnerable to pests, diseases, weather, and the like. But, in terms of old age, you shouldn’t have to worry about your tree declining.

Final Thoughts

Remember, every branch on your fruit tree should:

  • Have a purpose
  • Be load-bearing
  • Be fruit-bearing (ideally)
  • Be pest & disease-free

To learn more about pruning, check out this helpful video by Urban Homestead.


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