What to Prune in Late Fall for Healthier Trees, Shrubs and Perennials

When fall arrives, it's time to put the garden to bed. Late fall is ideal for pruning some plants but not all of them. Pruning perennials, trees and shrubs at the wrong time can trigger new growth that dies in cold weather, or it can cut off the buds needed for next year’s blooms. Bad timing can also leave openings for bacteria and fungi.

Done properly, pruning in late fall tidies up the garden, removes foliage where pests and diseases can overwinter and helps control the size and shape of plants. Just keep your pruning tools away from spring-flowering trees and shrubs like azaleas, lilacs, forsythias, magnolias, apple trees and hydrangeas that bloom on old wood, which includes oakleaf hydrangeas (Hydrangea quercifolia), mountain hydrangeas (H. serrata) and Bigleaf hydrangeas (H. macrophylla). Also, don’t fall-prune evergreen ferns, camellias, firethorns (Pyracantha) and coral bells, among other plants that add texture and color to the winter garden. Leave perennials like coneflowers, sunflowers, Black-eyed Susans, ornamental grasses (with some exceptions) and other seed or fruit-bearing plants that wildlife can use when food is scarce.

Browse our round-up of the best plants to prune in late fall, keeping these tips in mind:

• Wipe your tools with rubbing alcohol between plants to avoid spreading disease.
• Prune when it's mild and dry, so fungal spores are less likely to enter new cuts.
• Don't compost diseased or pest-infested trimmings. Trash them, so problems won't spread.

Late fall is a great time to prune bush, or herbaceous, peonies. Wait until after the first hard frost, when the leaves die or turn yellow and brown, and then remove them. Cut peony stems to one or two inches above the ground. Peonies are often plagued by powdery mildew, among other diseases, so getting rid of the foliage will help prevent them from overwintering in the soil. This is not the right time to prune tree peonies, however, unless you're simply removing dead stems, because peonies bloom on old wood. Late winter pruning is better for tree peonies. You can also trim lightly in early spring, although that may sacrifice some flowers. Some gardeners don't prune their peonies at all.

Like peonies, bee balm (Monarda) is susceptible to powdery mildew, so after the leaves die from a hard frost in fall, prune the plants to an inch or two above the ground. If they’re already infected with powdery mildew, cut them all the way to the ground to discourage this fungal disease from surviving in the soil all winter. Leave the stems of healthy plants alone, or shorten them, if you prefer, so hungry birds can snack on the seeds. Perennial bee balms will self-seed, so if you don't want more plants, remove the seedheads or take out the new green shoots when they emerge in spring. Powdery mildew affects garden phlox, too, so if your phlox plants are diseased, wait until the foliage turns brown in fall and cut their stems to 2 or 3 inches above the ground.

Daylilies varieties are available in many beautiful colors and sizes. After your blooms are finished, and all the buds on the stalks have opened, cut the flower stalks down to the base. This keeps the plants from forming seed pods, so they'll have more energy to grow and reblooming varieties can produce more flowers. After a late fall frost, when the leaves turn yellow or brown, or if they're looking tattered and unsightly, cut the leaves to 2 to 4 inches above the soil. You may be able to pull off the leaves by hand once they’re brown and dry, but be careful not to yank so hard you pull the plants up by their roots. Don’t prune your daylilies while most of the leaves are still green.

It helps to know what kind of perennial grass you're growing before you decide to prune: Is it a warm season, cool season or evergreen ornamental grass? Warm season ornamental grasses like pampas grass, switchgrass and perennial fountain grass turn brown in the winter, so some gardeners prefer to cut them to the ground in late fall to keep their gardens neat and tidy. Others leave them standing for winter interest or to provide seeds and shelter for wildlife.

However, if you live where there’s a risk of wildfires, protect yourself and your property by pruning ornamental grasses as soon as the foliage begins to dry out. It's also a good idea to remove diseased foliage as soon as you see it. If you're growing a self-seeding, aggressive ornamental grass that you need to control, cut it back before the seeds drop. If needed, wear gloves to protect your hands, and tie the cuttings into bundles for easier handling. You may need a hedge trimmer to power through thick grasses.

The rose is often called the "Queen of the Garden." For best results, don't prune your roses heavily in the fall, since that can stimulate tender, new growth that will perish in a freeze. But if your plants have very tall stems, you may want to shorten them, so they won't break or bend under winter's ice and snow. Strong winds can also damage tall roses by rocking the stems back and forth until the roots are loosened or even exposed.

To avoid damage, give tall stems a trim in fall. Prune them back by about 1/3, cutting at a 45-degree angle about 1/4-inch above outward-facing buds. To prune shrub roses to shape them or manage their size, wait until after several hard freezes and cut while they’re dormant in the winter or very early spring.

Knock Out roses are shrub roses that bloom on new growth. Deadhead the faded flowers and lightly trim them in fall, if needed, but avoid any serious pruning. Don’t prune climbing roses in the fall, unless you simply need to shorten very long stems so the wind won’t whip them back and forth.

Bearded iris bloom in spring, and some varieties bloom again in fall. When your rebloomers are finished, cut the flower stalks all the way to the base of the plants. Make the cuts at an angle, so moisture or rain can drain away instead of pooling, which can lead to rotting and disease. Removing the stalks also lets more sunlight and air reach the center of the plants.

It's time to prune the plant's leaves in fall. After you remove any that are dead or diseased, cut the remaining leaves straight across, 4 to 6 inches above the soil line, or shape them into fans for a neater look. To make the fans, cut the outer leaves 2 or 3 inches above the ground, and the inner ones to 4 to 6 inches, so they form a peak.

Dahlias are hardy in USDA Gardening Zones 8 to 11, so it’s usually safe to leave the tubers in the ground to overwinter if you live where the winters are mild, dry and warm. For extra protection, mulch them with 4 to 7 inches of mulch or compost.

In Zones 3 to 7, gardeners often treat dahlias as annuals. Others prune their dahlias in late fall to dig and store them. To prune in the fall, wait 3 to 5 days after the first hard frost and the foliage turns black or brown. Next, snip the stems to 4 to 6 inches above the soil. Gently pry up the clumps with a garden fork, being careful not to damage the roots. Shake or rinse off the dirt, let the tubers dry in a warm place for a few days, and box them up to store in in a dry, dark place that stays around 40 to 50 degrees Fahrenheit.

Got slugs and snails? You might if you forget to prune your hosta leaves before cold weather makes them soft and mushy. Hostas are hardy in Zones 3 to 9, so the roots can survive freezing weather across much of the US, but when the temperatures drop and the leaves turn yellow and floppy, they create an inviting pile of dead foliage for garden pests.

To avoid unwelcome visitors, cut the plants to the ground when the foliage starts to die. You can cut off the flower stalks at any time to direct more of the plants’ energies to their leaves and roots, although some gardeners keep the flowers for pollinators like bees and hummingbirds.

Slugs and other pests also like to make winter homes in delphinums when the leaves die and stalks become dry and hollow, so put out the "no vacancy" sign by pruning the plants in fall. Wait until the leaves turn yellow and die, or until the first hard frost makes the foliage limp and brown. Then cut the main stems and leaves to about two inches above the soil. If you live where the winters are very cold, you may want to protect the crowns of the plants by applying a thin layer of mulch or compost.