Fall Garden Clean-up

Several things can be done to prepare the garden for winter and the following growing season when fall arrives.


No Need to Clear Cut the Perennial Garden

It is not necessary to clear-cut the perennial garden after the first freeze of the season.  Leaving the leaves, stems, dried flowers, and seed heads of many perennials provides more interest through the winter months.  Leaving the plant materials also provides an extra layer of protection for the crown and root system of the perennial. Plus, the dead stems and leaves collect fallen leaves, adding even more protection.  Leaving the plant material in place and removing it in early spring instead of fall also helps provide food and protection to native pollinators, beneficial insects, and wildlife, like birds.  While it is largely beneficial to leave the foliage in place through winter, removing plant material in the fall after it has naturally died back should be done for perennials with disease or insect pest issues during the summer.  Additionally, those perennials that tend to be weedy or spread aggressively by seed benefit from late-season deadheading and clean up to prevent them from being too weedy.

Consider a Blanket of Mulch

Leaving plant debris in place over the winter months can help shallow-rooted perennials that may frost heave. Frost heaving happens when the freeze-thaw cycle of the upper layer of soil works the crown and root system of the perennial plant out of the ground.  If more protection is needed to prevent frost heaving, apply about four inches of mulch over the crown of the plant after the ground freezes, typically by late November in much of Iowa.  Do not place the mulch on too early as it can slow plants from going dormant and make them more susceptible to damage from cold temperatures.  Remove the excess mulch “blanket” in early spring as soon as the top layer thaws, typically around mid-March in much of Iowa.

Protect Marginally Hardy Perennials

Tender perennials can also be protected with cages placed around the plants and filled with straw or leaves. As with extra mulch, place the protective layer late in the fall season and remove it in early spring.  Do not use Styrofoam cones or domes as they can cause premature warming in the early spring bringing plants out of dormancy early and making them more susceptible to cold damage.  Additionally, most plants will not fit under these cones without extensive pruning, and it is better to prune in spring rather than fall. 

Vegetable Garden

Good Clean-up is Important

Most edible plants grown in home vegetables gardens have serious disease and/or pest issues that can overwinter on plant debris, increasing its impact on crops in subsequent years.  Good fall clean-up is necessary in the vegetable garden removing all leaves, stems, fruit, and other plant parts after the first frost.

Annual Beds and Containers

Good Clean-up is Helpful

As with the vegetable garden, good fall clean-up is beneficial for containers and garden beds where annuals are grown to help prevent disease and pest issues and reduce unwanted reseeding of some annual species in future growing seasons. 

Plant Cool-Season Annuals

Consider planting cool-season annuals to keep color and interest into the late fall season. 

Decorate with Natural Materials for Interest Over Winter

Evergreen boughs, ornamental seed heads, decorative branches, and other materials can be arranged in annual beds, frost-proof containers, and window boxes to create interest all winter.  Empty and store those containers that are not frost-proof to prevent cracking over winter.

Woody Trees and Shrubs

Do Not Prune in Fall

While it may seem tempting, do not prune woody trees and shrubs in the fall.  Pruning encourages new growth, and when done in the fall, the new growth that develops will not be well hardened off for winter leading to more potential for winter damage.  The best time of year to prune is later winter and early spring (February through March in Iowa).  Tender plants like roses or butterfly bush will have dieback during the winter.  During mild winters, that dieback will be less severe, so leaving all wood in place allows for more the plant to potentially make it through the winter and for you to start with a larger plant the following spring. Wait until new growth begins to emerge in spring and prune these tender woody plants back to live tissue. 

Wrap Trunks of Young Trees

During the winter months, when food is scarce, rabbits and other rodents will chew and strip bark from woody plants.  Protecting woody trees and shrubs, especially young plants, from browsing is important.  Wrap young trees at least 36” up the trunk with tree wrap in late fall and remove the protection in spring.  Adding tree wrap has the added benefit of protecting young trees from sun scald which can cause thin bark to split and crack on sunny winter days.

Install Fencing to Prevent Animal Damage

Place cages or stakes around young trees to prevent browsing and antler rubbing from deer. Stakes and fencing must be at least four feet call to prevent antler rubbing.    Cages around shrubs can also prevent damage from rabbits and rodents.  Use rebar posts and 36” tall chicken wire pinned to the ground when needed.  Make sure fencing is at least three feet tall, as animals can get over shorter fencing if there is deep snow cover.

More Information

More information about other common tasks in the fall can be found at these links.




Links to this article are strongly encouraged, and this article may be republished without further permission if published as written and if credit is given to the author, Horticulture and Home Pest News, and Iowa State University Extension and Outreach. If this article is to be used in any other manner, permission from the author is required. This article was originally published on September 10, 2021. The information contained within may not be the most current and accurate depending on when it is accessed.