Fruit Tree Pruning Basics: How and When to Prune

By Richard Flowers, ACCNP, Green Thumb Nursery Ventura

Prune most backyard deciduous fruit trees (apple, pear, peach, plum, apricot, nectarine, cherry) during the dormant season in late winter, before new growth starts, to build a strong framework, open the canopy to light and air, and remove dead or crossing wood. The two cuts you will use most are thinning cuts, which remove a whole branch to open the tree up, and heading cuts, which shorten a branch to a bud to force new growth.

Why Prune Fruit Trees?

Pruning is not just tidying. It does real work for the tree: it removes dead, diseased, and crossing branches, opens the canopy so light and air can reach the fruit, and builds a strong framework of scaffold limbs able to carry a heavy crop.^[1] A well-pruned tree also stays open and accessible so you can harvest, thin, and spray safely. Removing vigorous upright water sprouts and the suckers that grow from the base or below the graft is part of the job too; see our guide to water sprouts and suckers on fruit trees.

When to Prune Fruit Trees

For most deciduous fruit trees, the main pruning happens in the dormant season, in late winter before the buds swell and growth begins. Dormant pruning is invigorating: with the tree’s energy stored in the roots, cutting now is answered with a burst of vigorous spring growth, which is exactly what you want when you are building structure on a young tree.^[1] Pruning in summer does the opposite and slows the tree down, which is why summer cuts are the main tool for keeping a tree small; for that approach see our guide to keeping fruit trees small. There is one important exception: apricots and cherries are best pruned in dry late summer (July and August in inland areas, August near the coast) rather than in wet winter weather, because the spores that cause Eutypa dieback are spread by rain and infect the tree through fresh pruning wounds.^[2]

Thinning Cuts vs Heading Cuts

Almost every pruning decision comes down to two kinds of cuts. A thinning cut removes an entire shoot or branch back to its point of origin, where it joins a larger branch or the trunk. Thinning increases light and air penetration, keeps the tree’s natural shape, and does not trigger a thicket of regrowth, so it is the cut you reach for most.^[3] A heading cut shortens a branch by cutting it back to a bud. In response, several buds just below the cut push out dense, often vigorous new growth, which is useful for forcing low branching on a young tree or for shaping.^[3] When you make a heading cut, cut about a quarter inch above a healthy, outward-facing bud and angle the cut away from the bud, so the new growth heads away from the center of the tree.^[3]

How to Remove a Large Branch (the 3-Cut Method)

A heavy limb can tear a strip of bark down the trunk if you cut it in one pass, so use three cuts. First, make an undercut partway through the branch from below, a foot or two out from the trunk. Second, cut all the way through from the top about two inches beyond the undercut; the limb drops cleanly and any tearing stops at the undercut. Third, make the final cut just outside the branch collar, the slightly swollen ring of bark where the branch meets the trunk.^[4] Do not cut flush with the trunk and do not leave a stub; a clean cut just outside the collar lets the tree seal the wound naturally.^[4]

Training Young Trees

How you train a young tree depends on the fruit. Many apples are trained to a central leader, a pyramid shape with one dominant upright trunk and tiers of scaffold branches, with the widest tier at the bottom so the lower limbs are not shaded; pears are usually trained to an open center or modified vase.^[5] Peaches, nectarines, apricots, and cherries are usually trained to an open vase shape with three or four main scaffolds and no central leader, leaving the middle open to light.^[6] Whichever system you use, the goal is the same: a handful of well-spaced, strong scaffold limbs around the trunk, with wide angles that can bear a crop without breaking.^[5]

Tools and Keeping Them Clean

Use clean, sharp tools sized to the wood: bypass hand pruners for small shoots, loppers for thicker branches, and a pruning saw for anything larger. Sharp, clean cuts heal faster than crushed or torn ones. Because pruning tools can carry plant diseases from one cut or tree to the next, disinfect the blades, especially when you cut out diseased wood or move between trees; clean off dirt and sap first, then wipe or dip the blades in 70 percent rubbing alcohol, or soak them in a 10 percent bleach solution for at least ten minutes.^[7] For trees prone to fire blight, such as apple and pear, UC recommends dipping your shears in a 10 percent bleach solution between cuts.^[8]

Common Pruning Mistakes

A few habits do more harm than good. Do not top a tree by cutting all the main limbs back to stubs; topping forces weak, crowded regrowth and leaves large wounds, and thinning cuts that keep the tree’s natural shape are almost always the better choice.^[3] Do not leave stubs or cut flush into the branch collar, since both interfere with the tree’s ability to seal a wound.^[4] You also do not need to paint or seal pruning cuts: university research finds wound dressings do not speed healing and can sometimes make decay worse, so a clean cut left open is best.^[4] Finally, avoid removing too much at once, which stresses the tree and triggers excessive regrowth.^[3] New to fruit growing? Start with our list of easy plants for beginner gardeners.

Ready to get your fruit trees in shape? Visit any Green Thumb Nursery location for quality pruning tools and bare-root fruit trees in season, and our garden experts will help you make the right cuts for your trees.

Fruit Tree Pruning FAQ

When should you prune fruit trees?

Prune most deciduous fruit trees during the dormant season in late winter, before the buds break. Dormant pruning encourages vigorous spring growth, which is ideal for building structure.^[1] Apricots and cherries are an exception and are best pruned in dry late summer to reduce the risk of Eutypa dieback.^[2]

What is the difference between thinning and heading cuts?

A thinning cut removes a whole branch back to its origin and opens the canopy without forcing dense regrowth. A heading cut shortens a branch to a bud and stimulates bushy new growth below the cut. Most pruning uses thinning cuts, with heading cuts for shaping and forcing low branches.^[3]

How do you cut off a large tree branch without damaging the tree?

Use the three-cut method: an undercut from below, a second cut farther out to drop the limb, and a final cut just outside the branch collar. Do not cut flush with the trunk or leave a stub, so the tree can seal the wound.^[4]

Should you seal or paint pruning cuts?

No. University research finds wound dressings and pruning paints do not speed healing and can even make decay worse. A clean cut just outside the branch collar, left open, lets the tree seal itself.^[4]

What tools do you need to prune fruit trees?

Bypass hand pruners for small shoots, loppers for thicker branches, and a pruning saw for large limbs. Keep them sharp and clean, and disinfect the blades with 70 percent alcohol or a 10 percent bleach solution when cutting diseased wood or moving between trees to avoid spreading disease.^[7]

Sources

• [1] UC Statewide IPM Program, Pruning and Thinning: ipm.ucanr.edu
• [2] UC Statewide IPM Program, Eutypa Dieback: ipm.ucanr.edu
• [3] NC State Extension, General Pruning Techniques: content.ces.ncsu.edu
• [4] UC Statewide IPM Program, Wood Decay Fungi in Landscape Trees: ipm.ucanr.edu
• [5] UC Statewide IPM Program, Training Apple and Pear Trees: ipm.ucanr.edu
• [6] UC Statewide IPM Program, Training Stone Fruit and Nut Trees: ipm.ucanr.edu
• [7] Iowa State University Extension, How Do I Sanitize My Pruning Shears: yardandgarden.extension.iastate.edu
• [8] UC Statewide IPM Program, Fire Blight: ipm.ucanr.edu

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