UC Master Gardener Program of Alameda County
University of California
UC Master Gardener Program of Alameda County

Pruning Fruit Trees

By Dr. Mark S. Brunell

A tree’s purpose in life is to make viable seed for the next generation, to get that seed dispersed into the environment, and to store enough nutrients to survive the winter and then manage some vigorous regrowth in the spring.  The purpose of the home gardener or orchardist is more about growing high-quality fruits in reasonable quantities, and growing healthy trees that are easy to harvest.  Pruning is one of several practices necessary to achieve these goals.

Unpruned vs. Pruned

A tree left to itself, unpruned, will grow quickly as a juvenile in the first few years, producing few or no fruit, but as age increases the tree will usually “settle down” and begin bearing fruit, at which time vegetative growth (production of stems and leaves) slows.  The tree will get larger over time (perhaps to 30 or more feet in some species) and upper leafy branches will shade the lower parts of the tree.  Shade will inhibit formation of fruiting wood (that is, flower production), and therefore fruit production.  As a result, fruit is eventually confined to the tips of the branches, where light is present, and on a tall tree harvesting these fruits can be very difficult and even dangerous, requiring a ladder.  Pruning will lower the tree’s height, and allow sunlight to penetrate down into the tree’s lower branches, promoting lower-height fruit production.  Sunlight penetration can also be necessary for proper fruit color development in some species.  An unpruned tree also has dense shoot growth, which limits air circulation, possibly leading to disease.

When of fruit-bearing age, most fruit trees make more flower buds than are desirable.  Too many flowers equal too many fruits, and their great weight can break branches.  Furthermore, excess fruit often leads to smaller fruit size, presumably being caused by provisioning many vs. fewer developing fruits with nutrients (feeding many vs. fewer mouths with a fixed amount of food, so to speak).  A further complication is biennial bearing, where heavy fruit set one year may inhibit flower bud formation, leading to a small crop the next year.  Pruning would remove many of the flower buds, and fruit thinning would further lessen the number of fruit.

A tree left unpruned may also possess diseased or damaged wood, or branches that rub against each other, conditions that can potentially shorten the life of the tree.   You may have a friend that has fruit trees and never prunes or thins them, and says they are doing “just fine”.  That person may have low expectations and be satisfied with the fruit as they are, however it is a fact that pruning will make the fruit easier to harvest (height and position of fruit), likely more disease free, have larger and higher quality fruit, and have improved structural support for the fruit.

Pruning does have drawbacks: it is time-consuming and requires some education and experience; it opens wounds that can lead to disease, and it could potentially spread disease; if too severe the yield of the fruit will be greatly reduced; and increased light penetration, especially in summer, can cause sunburn of the bark which can lead to insect attack or disease. 

Below ground

To achieve good fruit production, the tree must make carbohydrates by growing photosynthetic leafy shoots, and absorb water and nutrients (especially nitrogen) from the soil through the root system.  Therefore, good fruit production requires both a healthy and vigorous shoot and root system.  Pruning cannot correct for deficiencies caused by a weak or compromised root system, although it can rebalance the shoot and root proportions when planting a young tree.  In other words, a tree with root rot, drought stress or nitrogen deficiency will likely perform poorly no matter how well pruning is done.  In such cases, the problems associated with the soil and roots need to be addressed (or better yet prevented through correct planting and cultural practices). 

Time line and expectations

Growing and maintaining fruit trees requires patience and a willingness to cut and destroy newly formed plant organs.  Realistically, a newly planted fruit tree will not be (or should not be) bearing fruit in the first couple of years (time depends on species).  Allowing fruit to form in the first two years will only slow the development of a proper framework for the shoot system.  Also, the thinning of fruit, removal of flowers, or the cutting of newly grown shoots is a very difficult act to perform for many people.  A common issue is the fear of making the wrong cuts and permanently damaging the plant, but understanding the basic responses of the plant to pruning, and understanding what your goal is make pruning easier.  For younger trees, the worst a person could do is to set the tree back a couple of seasons before it bears fruit.  Even if the plant was chopped-off at ground level (seedling tree) or just above the graft union (grafted trees), latent buds would probably grow and a new framework could be built from these new shoots.

Basics of plant structure and growth

Correct training and pruning of a fruit tree requires some basic education on how plants grow and respond to cutting.  Every cut a gardener makes should be made for a good reason, and he or she should understand the consequences of the cut and overall purpose for the cut.  If in doubt, do not prune the tree. 

Nodes, internodes, and general plant growth:

All shoots possess nodes and internodes.  Nodes are the regions of the stem where leaves (and/or flowers) attach.  The interval of stem between two adjacent nodes is termed the internode.  When first produced by the growing point of the shoot (apical meristem at the shoot tip), internodes are extremely short, but after aging slightly they elongate rapidly, causing the shoot to lengthen.  Elongation of the shoot (and root) by growth of the apical meristem is termed primary growth.  Shoots get thicker and stiffen after secondary growth occurs.  Secondary growth results from activity of the vascular cambium (just beneath the bark), which adds wood to the stem, and also the cork cambium, which thickens the bark.  Woody plants always begin life with primary growth, and then begin secondary growth toward the end of the first year.  A tree will undergo both primary and secondary growth throughout its life.

If a spindly, weak branch is cut off half way, primary growth of that branch will be stopped (apical meristem removed), but later on secondary growth will thicken that branch stub and make it stiffer.  Buds on that stub will start to grow eventually, establishing new primary growth, but that original stub will continue to thicken over time. 


Buds are active or dormant embryonic shoots that can be classified by location (terminal and lateral) and contents (leaf, flower, and mixed).  Terminal buds (also called apical buds) are found on the tips of shoots, and lateral buds (also called axillary buds) are located at the nodes, just above the point of leaf attachment (the leaf axil, which is the angle between the leaf stalk and the stem).  Leaf buds (also called vegetative buds) grow into leafy shoots.  Flower buds grow only into a single flower or an inflorescence (cluster of flowers).  Mixed buds grow into a shoot possessing both flowers and leaves, and the leaves are generally subtending leaf buds.  Leaf buds are usually thinner and more pointed than the rounder, wider flower buds.  Pome fruits (apples and pears) have both leaf and mixed buds.  Stone fruits (peaches, almonds, plums, apricot, and cherries) have leaf and flower buds.  The arrangement of the buds and their exact contents varies with the species.

An additional bud type is the latent bud (also called an adventitious bud), which is buried under the bark, or even within the roots, and cannot be seen.  For the home gardener, such buds are a nuisance because they cause root suckering and “water sprout” growth (vigorous upright growth) from below the graft union; such growth should be continually removed.

Apical dominance:

The terminal bud makes an inhibitory hormone called auxin, which moves by gravity down the shoot and prevents the lateral buds just beneath the terminal bud from growing.  The effect of this hormone is to allow the stem to grow straight up without branching.  In nature, this is an adaptation which helps the tree reach the light when growing in a dense canopy.  Pinching (removal of the growing point or apical meristem, the source of auxin) is a well-known method of inducing branching in an otherwise unbranched shoot.  After pinching, the auxin level is greatly reduced, which promotes branching by allowing lateral buds to grow into shoots.  If a shoot is bent and tied down to the horizontal, auxin moves downward, to the lower side of the stem and inhibits buds there; however the top side of the stem is released from the auxin inhibition, allowing bud growth all along the stem, producing vertical water sprouts.  A branch growing or bent to a 45 degree angle will exhibit partial apical dominance, with just a few lateral buds becoming shoots.  Therefore, apical dominance can be controlled by either pruning off the terminal bud, or by adjusting the angle of the branch.  Different species have different degrees of apical dominance, with the sweet cherry and Japanese plum having the greatest amount.  Such species continually make upright, largely unbranched growth.

Long and spur shoots:

Long and spur shoots differ in their internode lengths and the types of buds they possess.  Most plants (and all fruit trees) have long shoots, which have elongated internodes and well spaced leaves.  Most fruit tree species also have spur shoots, which form in the axils of the leaves of long shoots.  A spur shoot is a short, stocky shoot that has much shortened internodes.  Spur shoots form on shoots that are two years old or older, and can be unbranched or branched, and can be extremely short or longer.  The peach, for example, is said to have no spur shoots, but they are actually present but are short-lived and extremely short, so go unnoticed.  The apple is the other extreme, with large, branched, long-lived spur shoots.  Spur shoots are important because flower buds or mixed buds (and therefore fruit) largely occur on these shoots.  Long shoots can also bear flower buds or mixed buds, depending on the species and/or variety.

Pruning concepts

Two kinds of cuts are used to prune fruit trees: heading and thinning.  Both are required because without heading, the trees will not make the needed branches and will grow too tall, and without thinning the growth is too dense and will shade lower wood, which inhibits flower bud formation.  Heading cuts leave a stub behind, and involve removal of part of a shoot by cutting about ¼ inch above a lateral bud.  Heading cuts stimulate growth of buds (branching) below the cut, because apical dominance has been removed.  Too much growth from a heading cut can reduce sunlight penetration lower down in the tree.  A variant of the heading cut is the bench cut (also called “cutting back to lateral shoots”), where heading occurs immediately above a lateral branch that is directed in the desired location or angle.  In open center training, for example, we want growth to move upward and outward, so a bench cut placed just above a lateral pointing upward and outward could be used to achieve this.  Bench cuts generally do not stimulate the growth of additional branches below the cut, whereas a normal heading cut would.  Thinning cuts remove entire shoots, leaving no stub behind, and they reduce branch crowding and increase air circulation and sunlight penetration into the lower parts of the tree.  Thinning cuts are also used to establish the main scaffold branches of the tree, by removing unwanted lateral branches during initial tree training.  A tree made less dense by thinning is also easier to treat with pesticide sprays.

When choosing which branches to thin, consider branch angles.  Generally, you want a branch to be at an angle between 45 and 60 degrees, because it will develop into a very strong branch that can bear the weight of the fruit.  Branches with a narrow angle, less than 45 degrees, can be bent down to the proper angle when they are young and flexible, using toothpicks, sticks, clothespins, or by tying them down.  Branches at a narrow angle that have hardened and can’t be bent are probably best removed.

Young trees

The purpose of training the young tree is to develop a strong framework of well-spaced, properly angled branches on which all subsequent shoots and fruits will grow, and to produce a shape that allows sunlight penetration into the tree’s interior.  Several years may be required to properly develop a fruit tree’s branch framework.  During the training period, flowers that form should be removed, allowing all energy to be directed into the root and shoots.

Once the young tree is planted, the first step is to make a heading cut at 18 – 36 inches from the ground.  If some lateral branches are already present on the tree, keep the ones that are well placed and that have wide branch angles, and head them back to about 3 buds.  The dormant buds just below the heading cut will grow once spring arrives, and you will be presented with a series of lateral branches to work with.  In the common types of training, three or four of these laterals will form the scaffold branches, and we want them to be well distributed radially around the tree, and also well distributed vertically, with wide branch angles.  Scaffold branches arising from the same vertical position on the trunk form a very weak connection and will likely split apart under fruit load.

In the open center type of tree form, delayed heading is a method of ensuring the development of several lateral branches with wider crotch angles.  The unbranched young tree is headed, as discussed above, and is allowed to grow several branches just below the cut.  The branches that form immediately below the cut will have very narrow crotch angles, as they are assuming the role of the new central leaders.  This cluster of upright growth produces auxin which moves down the trunk to the lower-down lateral branches.  Auxin accumulates in the upper side of the crotches of these branches, which stimulates cell growth, forcing the crotch angle to widen.  Once the vertical shoots reach about 10 inches long, the trunk is again headed to remove this cluster of upright shoots.  What remains are the lower laterals which have wide crotch angles, suitable as scaffold branches.

The height of the lowest branch will be determined by the first heading cut made.  If you desire a taller tree that you can sit under, make the first heading cut up higher.

Once the young tree is planted and headed, it is a good idea to paint the trunk and/or branches with 50:50 water:white interior latex paint, which will help prevent sunburn.  Also, dig a few inches below the soil surface and paint that part of the trunk too (the soil will likely settle and expose the base to burning).

When to prune

It is probably true that most people prune in the dormant season, because seeing the branching structure of the tree is much easier and identification of flower and mixed buds is far simpler.  However, summer pruning has many advantages, such as the increased speed at which the branching framework of the tree can be developed.  Removing unwanted branches in summer redirects the tree’s energy into the branches that are desired, and hastens their growth.  Heading back primary scaffolds in the summer will promote development of secondary scaffolds soon after.  Opening up the structure will allow sun to penetrate the lower wood, promoting fruit bud formation.  Summer pruning has a devitalizing effect on growth, that is, the bud growth below a heading cut made in the summer will be far less than it would be if the cut had been made in the dormant season.  As many fruit trees are too vigorous in their growth, this effect is desirable.  Dormant pruning is best done just before bud break in the spring.  In summary, it is a good idea to do pruning in both the dormant season and at least once during the summer.

Tree forms

Fruit trees can be trained into many different forms, but two forms dominate in home gardens: open center and central leader.  Open center (also called open vase or bush) is used mostly for the stone fruits (peaches, nectarines, apricot, plum, and cherry), although any fruit tree species can be trained successfully using this system.  Central leader (also called dwarf pyramid) is generally used for apples and pears.

Open center:

Open center is the most widely used tree form for fruit trees in the home garden.  The main idea is to create spreading growth that is upwardly and outwardly directed, either by pruning and/or branch bending.  The center of the tree is kept relatively free of shoots from the very beginning of training; however care must be taken to avoid sunburn of exposed bark.  Correct early training (keeping the center open) and keeping some foliage in the center during summer pruning will help prevent sunburn (and the insect attack that will likely follow).  If burning is likely, protect the bark by painting with diluted white paint.

Once the headed young tree forms lateral branches, select 3 to 4 scaffold branches during the first growing season, and head back all other shoots to about 4 inches.  Avoid completely removing unwanted shoots, because the shade they provide will help prevent sunburn of the bark.  Once growth of the scaffolds has progressed (about mid-summer), head them at about 2 feet (or longer if desired and provided the scaffolds are stiff enough) to start development of secondary scaffold branches.

In the first dormant season after planting, complete any pruning that was not done in the summer, that is, finish the selection of scaffolds, remove any upright growth in the center, and remove short branches that are not needed.  In species that are naturally upright in their growth, now is a good time to bend down scaffold branches that are too vertical, or make bench cuts back to flatter-angled lateral branches.  For those species more inclined to branch and spread widely, it may be necessary to remove branches that are too flat-angled.  For the secondary scaffold branches, it is desirable to have about two per primary scaffold branch, with each secondary pointing up and away, but in different directions if possible.  When the secondary scaffolds reach about 2 feet in length (during next summer), head them back to produce tertiary scaffolds, and again select about two of them per secondary scaffold, positioned up and outward but in different directions.

As time goes on, the center of the tree will produce vigorous upright water sprouts which should be thinned out completely.  For branches that are incorrectly angled or pointing inward, continue to head back to a couple of buds (which helps shade the trunk).  As branch growth gets dense, occasionally thin out shoots to reduce crowding.  As the tree matures into bearing condition, it is important to understand the position and appearance of the flower buds or mixed buds, and the location of spurs if present.  When you are pruning, you must decide to remove or keep flower or mixed buds, and also how the pruning you are doing now will influence flowering later on.  The idea is to moderate the fruiting each year and avoid heavy crops of fruit.  In some species, heavy fruit set will reduce flower bud production, leading to lower fruiting the next year (biennial bearing).  By pruning out some flower buds now (and also by fruit thinning), you can work toward having a moderate crop each year.  Refer to the species section below for information on flowering habits of the major fruit tree species.

Central leader:

In a central leader tree, the goal is to form a tree resembling a Christmas tree in shape, which is wider at the base and narrower at the top, with a continuous trunk running from bottom to tip.  In this system, “whorls” of 3 - 5 branches (scaffold branches) form “tiers” along the main trunk, with about 3 feet between tiers, so that the first set of branches starts about 18 to 36 inches above the ground, then above that another tier of branches, which are shorter than those in the first tier.  Next is the third tier, which has shorter branches than the second tier.

In the initial training of the young tree, after the first heading cut several laterals will grow.  Choose the topmost lateral that is growing most upright as the new central leader. This branch will grow vertically and create the trunk between the first and second tiers, and it will also produce auxin that will widen the crotch angles of the branches below.  For the remaining laterals formed by the heading cut, choose three to five of them, well spaced radially and vertically, to form the first tier.  Head back each of these to about 3 buds, and thin out all other branches.  The new central leader may weaken or be outcompeted by other branches, so bend down competitors to reduce their inhibitory influence on the central leader.  If the central leader becomes weak, heading will invigorate its growth by forcing new, more vigorous buds to grow.  Each new tier is created by a new heading cut, which in turn creates a new whorl of branches.  Continue this process until the tree reaches the desired height, at which point the height is maintained by heading.  Each tier should be narrower in width than the next lower tier.

Species: flowering habits

Apple and Pear:

These are the pome fruits.  They possess leaf buds and mixed buds.  Apples produce an inflorescence (cluster of flowers) that possesses 5 – 6 flowers, and is determinate (oldest flower is at the center or tip of the inflorescence), whereas pears produce an inflorescence that bears 7 – 8 flowers and is indeterminate (oldest flowers are lateral, not central or at tip).  In apples, developing fruit tends to inhibit flower formation on nearby shoots, resulting in biennial bearing, whereas pears do not usually have this problem.  In both species, flower bud formation begins in summer.  Mixed buds are usually produced at the tips of spur shoots that are 2 years old or older (in apples, occasionally they are laterally produced on one-year old shoots).  In both species, occasionally mixed buds are found terminally on long shoots – these are the tip-bearing varieties.  When pruning apples and pears, care must be taken to not remove much older wood because that is the site of fruiting spur development.  Therefore, on mature trees about 20% of the new growth can be removed.  Remember that one-year shoots today will be 2 year old shoots next year, and will then start spur growth.  You must allow some new wood to remain on the tree to ensure future fruiting, but you also want to limit such vegetative growth so that reproduction is favored.  Fruiting spurs tend to be long-lived, but when older they will become congested and unfruitful.  Periodically, older spur systems should be reinvigorated by thinning out.  On tip-bearing varieties, pruning should be very light because the fruits form at the tips of long shoots.

Plum and Apricot:

Both plums and apricots have flower buds that are lateral in position, whereas leaf buds are both terminal and lateral.  Both species initiate their flower buds in late summer, and both flower before the leaves are present.  In both species, flower buds are produced on the current season’s shoots and on 2 year and older spurs (which are stubby).  In plums, each flower bud produces 1 – 3 flowers, whereas in apricots one flower is produced from each flower bud.  The Japanese plum makes a lot of vegetative, vertical growth each year so heading cuts are needed to maintain the correct height.  Avoid removing too much older wood, which bears the bulk of the fruit.  Pay attention to the location of the spurs and leave enough for a reasonable crop of fruit.  Neither species suffers much from biennial bearing.


Peach differs from other stone fruits in that flower buds are only produced on the youngest wood, that is, wood produced during last year’s growth (one-year wood).  Therefore, abundant young wood is needed to ensure a good fruit crop.  If you are dormant pruning and you remove almost all of the one-year wood, there will be almost no crop next summer, whereas such pruning in a plum would not severely lower the crop.  When pruning peach, it is a common practice to remove about half of the new growth each year, which will leave many flower buds for next summer’s crop, and stimulate the growth of new wood for the following year’s crop.  Spurs are not noticeable on peach; however a node will usually have three buds: two lateral flower buds and one central leaf bud.  Also, three leaves are often found at such nodes.  Terminal buds are leaf buds.  Flower buds each produce a single flower; therefore if each lateral bud at a node produces a fruit, the result will be two fruits with a shoot growing out from between them.  Peach flower buds start forming in midsummer; this species has a slight tendency toward biennial bearing.

Sweet Cherry:

Cherry produces flower buds borne on lateral short spurs that form on 2 year old and older wood, or at the base of long shoots.  Each cherry flower bud produces a few flowers (generally about 3).  Flower initiation occurs in the summer; however, flower buds tend to develop when their subtending leaf opened early in the summer.  Since the fruit size is small in this species we want to leave a lot of flower buds during pruning.  The biggest issue with this species is the pronounced apical dominance, so attention and effort must be given to making the growth spread upward and outward.  Heading cuts and bending branches can be used to achieve this growth pattern.

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