Complete Guide to Fall Garden Cleanup

Cleaning up flower beds and vegetable gardens in Autumn is a an annual chore to keep your garden tidy, and nice looking. Plus, it is much nicer to start of Spring right with a clean vegetable garden that is ready for planting. In this article I’m going to rundown the list of jobs you should, and shouldn’t do to your garden in Fall.

To help you quickly navigate this article, you can click on the links below to jump to various sections.

General Garden Clean Up

Before we get started on cleaning up our gardens, we should take a minute to gather some necessary materials. Assembling your tools prior to starting work can save time by eliminating multiple trips to the garage or shed to get that one tool you forgot.


  • Wheelbarrow
  • 5 Gallon bucket (to hold all your tools)
  • Small garden shovel or trowel
  • Hand pruning shears
  • Gardening shears
  • Hand weeding tool
  • Gardening gloves

Determine where you will put the waste

Cleaning up a garden usually results in a decent amount of dead plant material/waste. So, think of a place in your garden or compost area where you want to dump it. Otherwise, consider purchasing some yard waste disposal bags.

Cleaning up a vegetable garden in Fall/Winter

A vegetable garden can look quite unsightly after a couple of hard freezes! Most plants have produced their last fruit, and are looking pretty sorry!

Leaf mulch applied, and the vegetable garden is ready for Winter!

Remove Cages / Stakes

It is time to remove your cages or staking for vegetable plants such as peppers or tomatoes. Wipe them clean of any dirt, and store them in a shed, garage, or basement until the following year. Do not leave wooden stakes in the ground! They will rot and not be able to be used.

Remove dead plant material

Gather up all of your spent plant material, and either leave it in place to decompose, or take it to the compost pile. It will look nice if removed, but none the less it should be dealt with.

What to do with ‘diseased’ plant material?

You should compost all plant material, diseased or otherwise. Historically it has been advised to not compost diseased plant material. However, this advice is actually incorrect. The spores of fungus and other pathogens are ubiquitous and all over the yard/garden. You cannot escape them!

The key to not having various plant diseases is prevention. Try to avoid the conditions in which these diseases thrive, and you will stave off much trouble. Or, if you notice fungus starting on a part of a tomato plant, you should remove that leaf.

Spread Compost

Now is the time to spread a layer of compost all over your vegetable garden. Gather up your pile, and top-dress as much of your garden as you can. The nutrients and soil-life from your compost will add much fertility to your vegetable garden in the following year.

Spread that beautiful Compost!

Add Leaf Mulch

Adding a thick (6″) layer of leaves to your vegetable garden is the single easiest, cheapest, and best way to improve your soil’s fertility. The leaves will decompose in-place throughout the winter and next growing season. In addition to the added fertility, a thick layer of leaf mulch will serve as a natural weed barrier.

I’ve written about the benefits of leaf mulch before, as well as documented just how many nutrients are present in fallen tree leaves. I suggest you read those articles for more nitty-gritty details on just how much benefit you can get from leaves. But adding leaf mulch has been the single best thing I’ve ever done to improve my soil!

Video of how to improve soil with leaves

You should absolutely use Autumn leaves as mulch. They are usually available for free either from your own trees, your neighbors trees, or just go pick up some bags from the street!

Optional Fall Vegetable Garden Chores

Cover Crop

In early Autumn, you can plant a cover crop of soybeans, cowpeas or rye grass on your vegetable garden. The approaching winter will kill off these annual plants, leaving their root systems to decompose over the winter, adding fertility and organic matter to your soil.

Till in organic matter

This chore is not one I would do, as I think my rocky Pennsylvania soil will destroy the tines of any rototiller. Because of that I’m a practitioner of ‘no-till’ gardening! But- there are many people who grew up tilling their gardens in the fall. This can incorporate any weeds into the soil as organic matter, and that is a good thing. What it does to the soil structure is a subject for another article though.

Apply a layer of woodchips / mulch

If you have access to free sources of woodchips, from say a tree-trimming service or arborist. Then now is a great time to evenly spread a 4-6″ layer of wood chips to your vegetable garden. The woodchips will decompose inplace overtime, adding nutrients to your soil and greatly improving its fertility.

Overwinter pepper plants

Did you know that you can overwinter pepper plants? Now you do. This method is a nice way to keep your pepper plants alive during winter, allowing them to be replanted the following Spring.

Dig up your pepper plants, root ball and all. Then, prune the plant to just a 6″ stalk with only a couple of branches. And, make sure you remove all the leaves.

Then, pot it up in a 2-gallon pot with moist potting soil. And keep it in a location that will be around 50-60 degrees F. So, a garage or shed will work best. At this temperature the pepper plant will not grow much at all. Make sure the soil doesn’t completely dry out. But don’t worry about watering it too much.

Preparing a flower bed for Winter

Cleaning up a flower bed for Winter used to just mean cutting back all perennials to the ground, and removing dead annuals. But now we can make ‘fall cleanup’ a bit more ecologically friendly, while doing less work in the process, and still keep our beds looking nice.

Save seeds

Before you start removing dead/dormant plant material, you can start saving the seed! This is the perfect time to see if there are any plants you would like to gather a bit of seed from, and save for next year. Or, you can Winter-Sow the seed later around December/January.

BTW – Winter Sowing is the easiest way to start seeds! I highly recommend you check it out. Once you winter sow…you’ll never go back!

We’ve written a detailed guide on the dos and don’ts of saving flower seed. I highly recommend you have a look, as it is a great way to save money!

Anise Hyssop Seed Head seeds

Remove dead annual flowers

Annuals such as petunias, marigolds, and inpatients tend to die off not long after frost. These flowers will turn into piles of dead foliage quickly. So, just remove them to a compost pile.

Clean up a perennial garden

Perennial gardens are fairly easy to clean up in the Fall/Autumn. As a general rule, you can begin cleaning up perennial gardens once the flower stalks have gone dormant, which is usually after a couple of hard frosts. And since perennials are herbaceous, they can often be cut back right to the ground.

Typically I will remove dead flower stalks and dead foliage to a pile in the woods, to stay until Spring. But I only do this in perennial beds that are ‘prominent’ or can easily be seen from the curb.

Also, some perennials like Echinacea and Rudbeckia can look nice when dormant in the winter. So, leaving those can add some interest. Plus, leaving those flowers standing provides a food source for the birds (eating seeds) and overwintering habitat for some beneficial insects.

Do you need to cut back perennials in Fall?

Perennial flowers do not need to be cut back in Winter for the plant to survive. Any perennial will be just fine if you wait until Spring. Think of it like this, in nature nobody comes and prunes the plant after a couple of hard freezes. And the plant will return none the less. The stalks will fall and decompose when the time is right, usually in mid-Spring.

But flower beds that are featured prominently in the front yard can look better when dead plant material is cut back in the fall. Having scraggly plants/grasses next to your mailbox can be an eyesore. But, they don’t actually hurt anything.

In fact, there are some ecological benefits to leaving flowers up all winter.

Benefits of not cutting flowers back in the Fall

1 – Beneficial Insects over-winter in the stems

Certain species of insects will burrow into dead flower stalks to spend the winter. They will hibernate, so to speak, only to reemerge in the Spring.

2 – Birds will enjoy the seeds

Dried and dormant seed-heads of flowers feed the birds during the Winter. Numerous species of songbird will visit various species of flowers to pick out seeds during the cold winter months as their primary food source. Other animals will eat seed that falls to the ground.

Godlfinch perched on an Echinacea purpurea seed head

3- Dried flowers can look beautiful in winter

The fact is there really are some plants that look good standing tall all winter. Seeing snow collect on seed-heads of Joe-Pye Weed, Ironweed, Coreopsis, or seeing Big Bluestem grasses surrounded in snow is beautiful. And it is fun to see them sway under the weight of a songbird who is landing to eat some seed.

At our house, we cut back most flowers in beds that are located in our front yard and visible from the road. This is to please our neighbors and keep everything looking tidy. But there are some species that we will leave up. And any flowerbed that isn’t too visible from the road, we leave standing.

Apply a leaf mulch

Just like your vegetable garden, adding a leaf mulch is a great way to improve the fertility of your flower beds. The leaf mulch will also act as a natural weed barrier! Just put a 6″ layer of leaves on your flowerbeds, taking care not to cover the perennials.

Over the course of the following growing season you will have a natural weed barrier that feeds beneficial organisms and worms, as well as a new (free) source of organic matter that will improve the soil in your flower beds.

General Gardening Clean Up Chores / Tips

Pruning Trees and Shrubs

As a general rule don’t prune any woody shrubs or trees until there has been enough cold nights to kill off or send insects into hibernation. While it can be tempting to dive right in an improve the shapeliness of our trees and shrubs, we should refrain until insects have left for the season. Since most shrub and tree diseases are caused by contact with insects on the bare wood, we should wait until Winter has fully set in.

This is particularly important when it comes to certain species of tree such as Oak or Black Walnut. So, wait until the insects have gone for the year, then consider pruning shrubs or trees.

Clean up your tools

Brush any loose dirt off of your shovels. Use your garden hose to help loosen and remove any dirt from hand trowels and spades. You can apply a thin coat of 3-in-1 oil with a rag to help prevent rust from forming on the shovels.

Sharpen your pruning shears

One of the last chores should be to sharpen any hand pruners, shears, or similar tools. Get a flat file, or sharpening stone, and give new life to your tool. The easiest way would be to clamp the pruners in a vise, and just push (not pull) the file over the edge, trying to match the angle. As you push the file, move it along the blade length to keep the edge somewhat even.

If you don’t have a vise, you can always hold the tool down with one hand, and then push the file along the edge.

Also, you don’t need ‘razor’ sharp pruners! The sharper the blade the faster it gets dull. So, give it 20 passes with the file and (gently!) rub your finger perpendicular to the blade. If you can feel a nice difference in sharpness, you are probably done.

Winterize your lawn mower

Clean the underside of the mower

Turn off the fuel line (see the owners manual) and tilt the mower on it’s side. Use your hand or a plastic tool to scrape away grass and other debris. Finish it off by using the garden hose.

Change the oil

After all other garden chores are done, Fall is a great time for a little DIY lawnmower maintenance. Dust off your owners manual and change the oil and air filter of your lawnmower. Don’t forget to place a dab of oil on the spark plug to keep it functional after sitting all winter.

Also, Fall is also a good time to add fuel stabilizer to your lawnmower. This tutorial shows you how easy it is to do. And it is important! As most modern gasoline can gum up the carburetor and lead to a lawnmower that won’t start.

Sharpen the blade

Don’t forget to sharpen the blade on your lawn mower! This can make a huge difference in the cutting efficiency of your mower. Just follow the instructions in the owner’s manual to remove the blade, and sharpen it with a flat file.

Pound a nail into a stud and hang the blade on it to make sure it is balanced. If for some reason it keeps rotating to one side pointing down, that tells you that you need to take a couple more passes on that side.

Disconnect your hoses

One of the most important jobs to do for a ‘fall’ clean up is to disconnect your hoses. Leaving a hose hooked up in cold climates can result in frozen pipes! Not a situation you want to have in your home!

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Joe Foster

Hi - I grew up outdoors in nature - hiking, fishing, hunting. In high school I got my first job at a garden center where I learned to garden and landscape. I've been growing plants from seed and designing native plant gardens for over 10 years. I hope to share some of my knowledge with you! You may have seen some of my videos I create on our YouTube channel, GrowitBuildit (more than 10 million views!). You can find my channel here: Additionally I am a wood worker / DIY enthusiast. I enjoy designing/building projects (with hand tools when I can!). I hope to give you some tips and useful information!

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