As autumn paints the Hudson Valley and Finger Lakes in brilliant reds and golds, you might be wondering what to do with all those perennials that have given their all throughout the growing season.
But which ones should you cut back before winter arrives? The answer isn’t as straightforward as you might think!
While it’s tempting to grab your pruners and chop everything down to the ground, some plants benefit from fall pruning while others should be left standing until spring.
Today, we’ll look at 12 perennials that New York gardeners should cut back in the fall – and more importantly, why this timing makes such a difference for your garden’s health.
Since New York spans USDA hardiness zones 4a through 7b, from the chilly Adirondacks to the milder Long Island shores, these recommendations will help gardeners across the entire Empire State prepare their perennials for winter success.
1. Bee Balm (Monarda Species)
Let’s start with one of our most beloved pollinator magnets – bee balm! If you’ve grown Monarda didyma or any of its colorful cousins, you know how spectacular they are when covered in butterflies and hummingbirds. But what happens when fall arrives?
Even the most disease-resistant varieties of bee balm can succumb to powdery mildew by season’s end, leaving you with unsightly white-coated foliage. When that happens, you’ll want to cut the entire plant back to just a few inches from the ground. This prevents the disease from overwintering in your garden and gives the plant a fresh start come spring.
However, if your bee balm stayed healthy all season, you can be more selective. Try thinning out some of the older stems while leaving the seed heads for hungry birds.
The goldfinches particularly love Monarda seeds during those lean winter months!
2. Garden Phlox (Phlox Paniculata)
Garden phlox creates those dreamy cottage garden scenes we all adore, with their fragrant flower clusters in shades of pink, purple, and white. Unfortunately, they’re notorious for developing powdery mildew, especially during humid New York summers.
Cut back all foliage and stems in the fall, even if the plant looks relatively healthy. This simple step dramatically reduces disease pressure for the following year. You’ll want to dispose of the pruned material rather than composting it – think of it as taking out the trash to prevent uninvited guests from returning!
For best results, thin your phlox clumps every few years to improve air circulation. This helps prevent that pesky mildew from taking hold in the first place.
3. Bearded Iris (Iris Germanica)
Those spectacular bearded iris blooms that steal the show in late spring can become a liability by fall. The tall, sword-like foliage has a tendency to flop over as the season progresses, creating the perfect hiding spot for iris borers – one pest you definitely don’t want overwintering in your garden.
Cut the leaves back to about 6 inches from the ground, creating a neat fan shape. This removes potential pest habitat while leaving enough foliage to help the rhizomes photosynthesize before going dormant. Make sure to clean up all the debris around the plants, as fallen leaves can harbor both insects and fungal diseases.
If you noticed any soft spots or tunneling in your iris rhizomes this year, fall cleanup becomes even more critical for preventing future infestations.
4. Daylilies (Hemerocallis)
Don’t let the name fool you – daylilies aren’t true lilies at all! These workhorses of the perennial garden bloom reliably year after year with minimal fuss. While they’re not prone to serious disease issues, cutting them back in fall saves you from a messy cleanup job in spring.
Daylilies respond beautifully to what gardeners call “shearing” – cutting all the foliage back to about 4 inches from the crown. This is particularly important in areas where they don’t remain evergreen through winter, which includes most of New York state.
Focus especially on removing any yellowing or damaged leaves, as these can attract slugs and other pests if left to decompose around the plant base.
5. Peony (Paeonia)
Few plants create as much anticipation as peonies, with their spectacular late spring blooms that can stop traffic. But those same gorgeous flowers need a good cold period to set buds for next year’s display – which makes fall pruning essential for New York gardeners.
Cut peony stems back to about 2-3 inches from the ground once the foliage turns golden yellow (usually after the first hard frost). This timing is crucial because the leaves continue photosynthesizing and feeding the roots until that color change occurs.
Peony foliage is particularly susceptible to fungal diseases, so proper disposal of the cut material is important. Never compost diseased peony debris – it’s not worth the risk of reintroducing problems to your garden.
6. Blanket Flower (Gaillardia × Grandiflora)
These cheerful orange and red daisies bloom from summer right through frost, making them fantastic for extended color. Blanket flower is remarkably hardy, but cutting back the spent stems in fall seems to improve its overall vigor for the following season.
Trim the plants back to about 4-6 inches from the crown, removing all the old flowering stems. This encourages the plant to put energy into developing a strong root system rather than trying to maintain tired foliage through winter.
If you’ve been deadheading throughout the growing season (which promotes continuous blooming), you can leave some seed heads in place for winter bird feeding before doing your final fall cleanup.
7. Columbine (Aquilegia)
These delicate-looking perennials with their distinctive spurred flowers are surprisingly tough, but they benefit greatly from fall cleanup. Columbine foliage often shows leaf miner damage by season’s end – those characteristic squiggly trails left by tiny insects tunneling through the leaves.
Remove all damaged foliage and clear away any debris around the plant base. Columbine sends out fresh growth very early in spring, so fall cleanup prevents old, diseased material from interfering with new shoots.
To prevent excessive self-seeding (columbines are enthusiastic self-sowers), remove flower heads after blooming.
Leave healthy foliage until after frost, then cut back to the crown.
8. Catmint (Nepeta)
Your feline friends aren’t the only ones who love catmint – bees and butterflies find it irresistible too! This drought-tolerant perennial responds beautifully to pruning throughout the growing season, and fall cutting helps tidy up plants that will suffer winter damage anyway.
Cut catmint back to about 3-4 inches from the ground after the first hard frost. The silvery-gray foliage won’t survive New York winters intact, so getting ahead of the cleanup saves you work in spring when you’re eager to see new growth emerging.
Many gardeners cut catmint back by half in midsummer to encourage fresh growth and a second flush of blooms – if you did this, you might find less cleanup needed in fall.
9. Salvia (Salvia Nemorosa)
Perennial salvias are absolute stars in the summer garden, with their spiky purple, blue, or white flower clusters attracting butterflies all season long. These tough plants benefit from several pruning sessions throughout the year to prevent flopping and encourage reblooming.
When fall arrives and blooming slows down, cut the entire plant back to the new basal growth at the crown. This keeps the plant tidy through winter and prevents the old stems from breaking and creating a mess in spring.
Don’t confuse perennial salvia with annual varieties – we’re talking about the hardy Salvia nemorosa types that return year after year, not the red salvias you might grow as annuals.
10. Yarrow (Achillea)
Yarrow might be one of our toughest perennials, but it has one major weakness – it absolutely hates sitting in cold, wet soil during winter. This makes fall pruning particularly important for New York gardeners dealing with snow melt and spring rains.
Cut yarrow back to about 2-3 inches from the crown in early fall, before the worst weather arrives. By this time, most of the blooms are spent anyway, and the foliage often starts flopping or showing signs of disease.
The good news? New basal growth typically fills in before hard frost, giving you some green to look at through early winter while protecting the crown.
11. Painted Daisy (Tanacetum Coccineum)
These charming daisies in shades of red, pink, and white add cottage garden charm wherever they’re planted. However, painted daisies are prone to crown rot in wet conditions – a real concern during New York’s variable fall and winter weather.
Cut back all foliage after frost turns the plants brown. Good drainage is critical for these plants, so fall cleanup combined with proper siting helps prevent the wet-soil issues that can kill them over winter.
If you deadheaded throughout the season (which encourages reblooming), you’ve already done most of the work – fall cleanup is just about removing the remaining foliage and tidying up.
12. Hardy Begonia (Begonia Grandis)
Here’s one that might surprise you – not all begonias are annuals! Hardy begonias produce delicate pink or white flowers in late summer and fall, thriving in shaded spots where many other perennials struggle.
The key with hardy begonias is preventing crown rot from wet, decomposing foliage. Frost will blacken and collapse the leaves, and if left at the base of the plant, this soggy mess can kill the crown over winter.
Cut plants back to the ground after frost damage occurs, and clear away all debris. The underground bulbils will survive New York winters just fine if kept from sitting in wet, rotting organic matter.
Why Fall Pruning Matters in New York
You might wonder why timing matters so much when it comes to cutting back perennials. The answer lies in New York’s climate patterns and the specific challenges our gardens face.
Fall pruning helps prevent several common problems:
- Disease prevention: Many fungal diseases overwinter in dead plant material
- Pest control: Insects like iris borers hide in old foliage
- Crown protection: Removing soggy debris prevents root and crown rot
- Garden tidiness: Fall cleanup means less work when spring fever hits
However, remember that not all perennials should be cut back in fall! Plants like ornamental grasses, sedums, and coneflowers (Echinacea) provide valuable winter interest and bird food, so save those for spring cleanup.
When to Tackle Fall Pruning
The best time for fall pruning in New York typically falls between mid-October and mid-November, depending on your specific location. Wait for a hard frost to damage tender foliage, then choose a dry day for your pruning work.
Use clean, sharp tools and dispose of diseased material properly. If you encountered pest or disease problems during the growing season, clean your pruners with a bleach solution between plants to prevent spreading issues.
Looking Ahead to Spring
By taking care of these 12 perennials now, you’re setting your garden up for success next spring.
Clean, healthy plants emerge more vigorously, have fewer pest and disease issues, and often bloom more prolifically.
Next spring, when you see fresh green shoots emerging from those neatly pruned crowns, you’ll appreciate the time you spent this fall preparing your garden for winter.
After all, successful gardening is as much about knowing when to cut back as it is about knowing when to plant!
