Fall Cleanup or Not

Fall 2013
Sheep feed on a summer cover crop of Japanese millet, with another garden in the background. Photo by Eric Sideman
Sheep feed on a summer cover crop of Japanese millet, with another garden in the background. Photo by Eric Sideman.

By Eric Sideman, Ph.D.

Gardeners do not often think of themselves as managers, but they are. At this time of year, which I refer to as Fair time, gardeners have to make a very important decision about how they manage fall cleanup of their gardens. Farmers, who know they are managers, are also deciding whether to clean up crop debris or leave it in the field as organic matter to decay and build soil.  After all, every bit of organic matter does good, from feeding microbes in the garden to improving soil tilth. So leaving it seems like the better choice.  Sometimes it is not.

Factors included in the decision are which insects, plant diseases and weeds were in the garden, and what time of year you are done with your garden. Remember that you do not have to treat your entire garden the same. Just as farmers work different fields differently, you can clean and till parts of your garden and leave other parts covered with crop debris.

Managing the soil is at the heart of all decisions organic growers make. A guiding rule is that no soil should be left bare to get the brunt of weather for any longer than necessary. If you are done with a garden – or a portion of a garden – early in the season, then the best practice is to get rid of the crop debris and plant a cover crop.  If this happens early in the summer, I suggest planting buckwheat for a while followed by oats in very early September. If you are not finished with the plot until late summer, I suggest getting rid of the debris and planting oats. But if you are not done with the garden until mid- to late fall, then you may be better off leaving the crop debris to protect the soil.

Protecting the soil is the guiding rule, but all rules may be broken given a good enough reason to do so – such as weeds, insects or diseases that may wipe out your crops. Here are a few examples from the long list of gardening problems that would drive me to clean up the precious crop debris late in the fall rather than leaving it to protect the soil.


The asparagus beetle hides for the winter in asparagus crop debris. If I have the beetle, I cut the asparagus fronds at soil level after they turn yellow and die in late fall, then rake up as much of the debris as possible to remove the hiding places. I do not recommend putting this debris in a compost pile, unless you know all parts of the pile will get hot.


The two most common garden tomato problems in our region are early blight and Septoria leaf spot. Both survive the winter in and on crop debris. Spores and fungal tissue in the debris are the initial sources of infection for the following year’s crop.  As soon as I give up harvesting tomatoes, I get rid of all of the debris. I am never sure that my compost gets hot enough, so instead of putting the debris in the pile, I really get rid of it by bagging or burying it. The following year, I either grow tomatoes in a new garden or mulch the ground so that no pathogen splashes up from the tiny bits of debris I missed.

Sweet corn

Sweet corn leaves a lot of debris that is loaded with good fibrous, carbonaceous tissue that is great for the soil biology. I want to leave it, but the European corn borer spends the winter in the stalk.  Since most of the borers overwinter in the bottom 6 inches of stalk, I cut the stalks at ground level and then cut them into small pieces with loppers. Most of the borers fail to survive in this chopped corn, because they are now susceptible to all sorts of predators and weather.


The squash bug and the cucumber beetle both overwinter in crop debris and in other debris near their summering spots. I try to get rid of all their hiding places by hauling away all the squash debris I can find. I am lucky to have a few gardens, so I never put anything in the squash family back in a garden two years in a row.

Peas and Early Beans

These are done by midsummer, when I till them in and plant a cover crop. Often the cover crop is something the sheep like, such as rape, tillage radish or Japanese millet, and it supplements the weak summer growth of pastures. When the sheep are done eating, there is still time for a fall cover crop.


I often have problems with Botrytis leaf blight and onion thrips. Both survive the winter in onion debris, so after harvest I till the crop debris in. This usually is early enough to then plant a cover crop of oats.


This horrible weed can take all the enjoyment out of gardening, and often out of the harvest, too. This cool weather grass grows best in spring and fall, so that is the time to beat it back with tillage – which is terrible for the soil, but sometimes the sacrifice is necessary in order to gain the upper hand. With a bad infestation of quackgrass, I recommend lots of fall tillage right into late fall. Every time the grass gets a few inches tall, beat it back. Then, when it has stopped growing (nearly Thanksgiving), spread some straw on the soil surface to protect it over winter. If quackgrass is still trying to grow in the spring (it will be among the first plants to green up), beat it back then, too. You can use that piece of ground for a late crop after you are sure the quackgrass is dead. You might also cover the infested area with a large sheet of heavy black plastic and then, the following year, transplant squash and pumpkin plants through holes in the plastic. Be sure to remove the plastic after the squash is harvested, because it is the perfect overwintering site for squash bugs.

Many more problems warrant a debris-removal management decision. Learn the biology of the pest so that you have the information needed to decide which option is best.

Eric Sideman, MOFGA’s organic crop specialist for many years, is now retired.

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