5 Reasons You Should Never Prune Your Trees in Fall

I bet you’re working on your fall to-do list, and I’m right there with you. But pruning your trees is something you should leave off that list until late winter. Join organic farmer Jenna Rich as she discusses five reasons you should never prune your trees in the fall.

A man's hand grips blue pruning shears as he cuts bare tree branches in an autumn garden, with vibrant, colorful leaves softly blurred in the background.

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Fall is a time for gardeners to clean up their garden beds, sharpen and clean tools, organize sheds and greenhouses, and tidy up so they’re ready for spring chores. It might seem like a great time to prune your trees to get that off your to-do list, but doing so may undo much of the hard work you’ve done leading up to the fall to ensure your trees stay healthy and strong

When adding trees to your lineup, ensure they are compatible with your growing zone. Doing so will set them up for success and make caring for them more enjoyable. A tree out of its element and experiencing high stress levels won’t thrive, so checking that your region aligns with its needs will yield the best results. 

If you’re like me, your fall and winter checklists are in full effect. When all the items are checked off, I have peace of mind, which allows me to enjoy my winters and feel prepared for spring. Let’s discuss five reasons you should never prune your trees in the fall

Your Tree is Busy Preparing For Winter

A serene winter garden features a house surrounded by bare bushes and trees blanketed in soft white snow.
Trees prepare for winter’s challenges with internal adjustments.

Humans greatly enjoy watching the transition of summer greens to autumnal oranges, yellows, and reds, so it’s hard for us to understand just how hard the trees are working internally. It’s a significant endeavor that takes lots of energy. Think of everything you do around your home and property as the seasons change to refresh, prepare, and unload for the upcoming season.

Trees and perennial plants are doing something similar internally in preparation for the change of seasons. Imagine someone asking you to give a speech just as you fall asleep for the night. It probably wouldn’t be great, right? 

As their colors change and leaves drop, the trees’ energy shifts into their own fall chores, including sugar concentration, intentional dehydration, and cellular shrinkage. As they adjust to shorter days, colder temperatures, and less water, they slow their processes down to prepare for dormancy. Concentrated sugars serve as a natural anti-freeze, which helps them tolerate freezing temperatures, reduces the risk of them exploding from being too cold, and provides energy in the winter months. 

Cells shrink and harden, preventing damage from freezing temperatures and harsh winds. Surviving the winter in some regions is an impressive feat, so it takes a lot of preparation. Note that some species produce buds in the summer months that will overwinter just fine. Pruning too early may remove these, giving you a less-than-spectacular show in the spring. 

They Need To Focus Energy on Their Roots 

Fallen apples, both fresh and rotten, dot the soil around the roots of trees, creating a colorful display.
Healthy roots strengthen them for thriving spring growth.

We often discuss the need for a robust root system, which anchors plants to the ground, helps prevent topsoil and nutrient loss, and ensures proper growth and immunity response. When we prune during the fall transition period, we force energy into the wounded areas rather than allowing the tree to focus on its root system. This can be detrimental to the tree’s health and longevity. 

Instead, take advantage of the cooler working temperatures. Soil temps will remain warm, encouraging roots to expand and stretch deeper into the soil, well out of eyes’ reach. Once trees lose their leaves, they can hone in on underground activity. When they wake in the spring, deep, strong roots mean a healthy start to the season!

Damage From Fresh Wounds

Close-up of a man with pruning shears poised to trim the bare branches of a fruit tree in a garden, with a blurred background of green lawn.
They need time to heal naturally from wounds.

Imagine having a large, fresh cut on your arm and heading outside into the wind and cold weather without any covering. You can imagine the pain you might feel when the air hits the open wound. Trees may not “feel” the same way we do, but wounds, even from necessary pruning, are still wounds and should be treated as such. Remember also that several types of beetles are still active in the fall, and wounds may exacerbate their damage.  

The best time to prune is during dormancy when less activity is happening inside the tree, and the risk of disease spread is significantly reduced. Winter pruning encourages new spring growth. Wounds made over winter will heal more quickly during the spring months. 

Note: Spring flowering plants like azaleas should not be pruned until after they flower. Pruning in the winter removes fresh buds, so you’ll be without spring blooms. 

While it was once commonplace to see tree wounds closed up with white paint, updated research tells us to leave them be and let them complete their natural immunity response for best results. According to the University of Illinois Extension, trees will respond to a wound with wound tissue, which will seal the pruning cut.

Sealing it up with paint is detrimental since oxygen is required for this process to occur. Healthy specimens are more likely to ward off future attacks, so it’s our job to keep them as healthy as possible. 

Wet Conditions Promote Disease Spread

A close-up of a tree branch affected by Nectria canker, showing raised, orange-beige bumps on the bark.
Fall’s damp weather invites harmful pathogens.

Many fungal and bacterial pathogens thrive in fall’s wet, cool conditions. In many regions, fall brings cool, damp weather, wreaking havoc on freshly pruned trees and shrubs. These pathogens can easily creep into the open wounds when humidity levels are high.

Oak wilt, Nectria canker, Dutch elm disease, bacterial canker, fire blight, apple scab, peach scab, and blossom wilt are just a few diseases to watch out for in the fall. Proper pruning, copper sprays, and immediate removal of infected tree parts work to control some of these, but oak wilt and bacterial canker have no known proven home gardener treatments.

Trust your sources when bringing new trees to your property. Select disease-resistant varieties and grafts when available. Contact your local experts if you’re unsure what’s happening with your orchard. Swift action is always best! 

Keep your eyes peeled for elm leaf beetles (Xanthogaleruca luteola). These pests chew holes in leaves and may hibernate in the surrounding areas, ready to cause more trouble in future years. Unfortunately, this pest has few natural enemies, so prevention or chemical control are the only options. 

Pro tip: Always sanitize your pruning tools before and after use to prevent future spread, and avoid pruning when conditions are wet. 

You Don’t Want To Encourage New Growth Before Winter

Close-up of thin branches adorned with young green buds in a sunny garden.
Allow them to focus on their roots this winter.

New growth is green and vulnerable. Promoting new growth before winter exposes it to extreme conditions it’s not ready for. As mentioned, fall offers the perfect conditions for plants to focus on their root system. Leaving them be for a few months allows them to do naturally what they know to do. Let the tree close up shop for the year (and you do the same) and encourage new spring growth during winter pruning sessions

Waiting until the trees are bare of leaves allows you to see the shape more clearly and create an efficient pruning plan. You can see overlapping and twisted branches, growth outside the desired canopy shape, and dead or diseased limbs. 

Exceptions To The Rule

Light pruning may be recommended if your tree shows signs of disease or has lower branches near or touching the ground. Contact a local arborist or tree specialist at your local extension office for necessary assistance. 

A Note About Conifers

A gardener uses large pruners to trim the dense, green foliage of a spruce tree.
Evergreens stay green, adapting to seasonal weather changes.

Spruce and pines retain their needles all year and don’t enter full dormancy like deciduous species. Pine needles retain more moisture and allow them to convert sunlight into chlorophyll all year, which is why they are sometimes called evergreens. 

While they don’t entirely go dormant, their bark and branches offer insulation and protection from the cold, so they should be pruned in spring like deciduous trees for best results. 

What To Do In The Fall Instead

The gardener gathers dry leaves, branches, and weeds into a pile to clean the garden of debris.
Prepare your garden for winter with thoughtful maintenance practices.
  • Clean up garden debris 
  • Determine your mulching plan 
  • Amend your soil so it’s ready for spring
  • Cover crop to suppress weeds and reduce soil erosion
  • Be patient until your trees are in dormancy to perform pruning

Are you stuck on which trees to choose? Consider low-maintenance trees like winterberry holly, witch hazel, and serviceberry, which will still provide shade, beauty, pollinator attraction, and height

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