Pruning a Young Apple Tree: Your First Three Years, Cut by Cut

The Three-Year Plan at a Glance

To prune a young apple tree, cut an unbranched whip back to 30 inches at planting. The next late winter, keep one central leader and 3 to 4 wide-angled side shoots as the first tier of scaffold limbs. In the second and third years, keep a single leader and add a new tier of branches 24 to 30 inches above the last. Those figures come from Iowa State University Extension, and the rest of this guide walks through each cut.

The shape this builds is called a central leader. One trunk runs up the middle, and tiers of side branches, called scaffolds, come off it with the widest tier at the bottom. Iowa State describes the finished tree as having 3 to 4 tiers, with 3 to 4 branches in each of the lower two and only 2 or 3 in the upper ones.

When	What to cut	Source figure
At planting	Head the whip	30 inches above ground
First late winter	Keep the leader and 3 to 4 scaffolds; shorten both	Scaffolds back by 1/4, leader by up to 1/2
Second late winter	Choose a second tier; spread the first	24 to 30 inches above tier one; 45 degrees
Third year on	Repeat upward; keep one leader	3 to 4 tiers in the finished tree

When to Prune

Prune for structure while the tree is dormant, in late winter or early spring. The month depends on where you live, and three extension services give local windows:

• Iowa: March and early April (Iowa State).
• Virginia: late winter, after the threat of severe cold (Virginia Cooperative Extension).
• North and central New Mexico: February to early March (New Mexico State University).

If your climate is closer to one of those than the others, use its window. In all three the principle is the same: wait until the worst cold has passed, and finish before growth starts. The late-winter pruning guide covers what else in the garden gets cut in the same window.

The Two Cuts You Need

Nearly every cut on a young tree is one of two kinds, and they have opposite effects.

A heading cut removes the end portion of a shoot. New Mexico State’s pruning guide notes that it removes part of a branch and stimulates new growth, which is why you head the whip and the leader when you want side branches to form below the cut.

A thinning cut removes an entire shoot or branch at its point of origin and does not stimulate new growth. Use it to take out a competing leader, a badly angled shoot or a branch in the wrong place.

Make thinning cuts close to the branch collar, the point where a branch joins the trunk or another branch. New Mexico State describes the collar as the wrinkled, swollen area at the base of the branch, holding the tissue that seals the wound. The same guide states that when pruning is done at the right time with sanitized tools and proper technique, trees heal themselves and wound dressing is not necessary. Our guide to choosing pruning shears covers what to look for in a pair, and a clean cut depends on an edge kept up as described in sharpening pruners and loppers.

Year One: At Planting

What you do on planting day depends on what came from the nursery.

An unbranched whip. Cut it to a height of 30 inches. Iowa State, Virginia Cooperative Extension and University of Illinois Extension all give that figure. New Mexico State gives a range of 29 to 36 inches for spur-type and semi-dwarf trees. Heading forces buds below the cut to grow, and Iowa State notes that a central leader and several side shoots will develop on the upper 8 to 10 inches of the trunk by summer.

A branched tree. Some nursery trees arrive with side branches already formed. Keep the ones that are well placed and have wide angles, and remove the rest with thinning cuts. Illinois advises choosing branches with wide crotch angles that arise between 18 and 28 inches from the ground.

Angle matters from the first season. Virginia Cooperative Extension states plainly that limbs with narrow crotch angles are weak, and that angles can be improved by spreading newly developing shoots in spring with toothpicks or pieces of wire. New Mexico State suggests clothespins for the same job when the shoots are 5 to 6 inches long and still flexible. Attach the clothespin to the trunk so it lies on top of the new shoot and holds it flat.

Year Two: The First Late Winter After Planting

This is the session that sets the lowest tier. Iowa State’s steps are:

1. Keep the central leader, the most upright shoot at the top.
2. Select 3 to 4 well-distributed side shoots with wide crotch angles. The lowest should be approximately 2 feet from the soil surface.
3. Remove the other side shoots.
4. Cut back the selected side shoots by 1/4 and the central leader by up to 1/2.

“Well-distributed” means spaced around the trunk, so that no branch sits directly above another. If two upright shoots are competing for the top, keep one and remove the other completely. Virginia’s guide takes out competing leaders during the dormant season.

Illinois puts the count a little differently, noting that after one growing season two to four scaffolds can usually be selected. If your tree made only two good shoots, keep those and pick the rest next year.

Year Three: The Second Tier

After the second growing season, the leader has extended and thrown a new set of side shoots higher up. Iowa State places the second tier of scaffolds about 24 to 30 inches above the top branch of the lower tier. Choose branches there the same way as before: wide angles, spaced around the trunk, and not directly over a first-tier limb.

This is also when Iowa State brings out limb spreaders. After two growing seasons, use them to push the first-tier scaffolds out to a 45 degree branch angle, and leave the spreaders in place for 2 to 3 years. Virginia notes that spreading older scaffolds may take spreaders 3 to 4 feet long.

Keep heading the leader each dormant season. Virginia’s instruction is to head the one-year-old section of the central leader by removing 1/4 to 1/3 of the past season’s growth, which keeps it vigorous and stiff and encourages branching above the first set of limbs. Virginia also advises removing fruit from the central leader to prevent it from bending.

Dwarf, Semi-Dwarf and Standard Trees

The tiered plan above suits a freestanding tree with room to grow. On smaller trees, extension guides often space scaffolds continuously along the trunk instead of in separated tiers, and the numbers shrink with the tree. University of Illinois Extension gives these targets:

Tree size	Trunk height	Scaffolds	Vertical spacing
Dwarf	4 to 6 feet	6 to 10	2 to 6 inches apart
Semi-dwarf or spur-type	5 to 8 feet	6 to 12	4 to 8 inches apart
Standard	6 to 10 feet	10 to 15	8 to 15 inches apart

For dwarf and semi-dwarf trees, Illinois sets the lowest scaffold at about 18 to 22 inches above the ground. Check the tag for the tree’s size class before choosing which plan to follow, and stick with one source’s numbers instead of mixing the two systems. Size class comes from the roots the tree is grafted on, which is explained in choosing an apple tree rootstock.

Mistakes That Cost Years

Three errors account for most of the corrective pruning that young apple trees need later.

Skipping the heading cut at planting. The cut at 30 inches is what produces a leader and side shoots in the top 8 to 10 inches of trunk, at the height where the first tier belongs.

Keeping narrow-angled limbs. A scaffold with a tight angle is weak at the joint. Spread shoots while they are 5 to 6 inches long, or choose a different branch.

Leaving the lowest branch too low or too high. Iowa State aims for about 2 feet, and Illinois gives 18 to 22 inches on a dwarf or semi-dwarf. Virginia ties the height to mowing: most commercial orchardists prefer the first branches 24 to 26 inches above ground, and for a tree grown in a yard it recommends 30 to 36 inches.

Once the framework is built and the tree starts to carry a crop, the next skill is covered in thinning fruit on apple and peach trees.