Ask a Master Gardener: Veggie Garden Clean Up

final tomato harvest

Hello and happy pumpkin spice season to those of you who celebrate! (I definitely do.) This summer went by quickly, but what could be better than pumpkins, hooded sweatshirts and fall colors? How about potato leek soup with frost-kissed leeks from the garden, or an entire stalk of brussels sprouts? I hope you’re savoring harvest season as much as I am.

Q: Should I clean out my vegetable garden in the fall, or leave the dead plants there all winter and clean them out in the spring?

leek harvest

Jennifer harvests her leek crop.

A: This is a great question, especially for new gardeners who might see conflicting information about leaving the leaves or providing winter interest. I am a big fan of leaving my perennial areas—especially the native plantings—a little messy for the winter. But when it comes to vegetable gardens, it’s a different story.

Vegetables, for the most part, are tropical plants that did not evolve to grow here in the cold north, even though they’ve been cultivated successfully here for ages. Because humans have been growing them in such large numbers and for so long, pests and diseases that target these plants tend to spread around and stick around. One thing that helps us avoid them is careful crop rotation, but the other is cleaning up plant debris at the end of the season so bacteria and viruses won’t overwinter in the soil.

Both minor inconveniences like powdery mildew and bigger problems like verticillium wilt, fusarium wilt and mosaic viruses can all overwinter in your soil. Some viruses are downright nasty; tobacco mosaic virus, for example, can persist in soil for up to 100 years!

My cucumbers frequently get blight and/or powdery mildew in late August or early September. I don’t wait very long to pull the whole plant and give up for the year when this happens. To be extra safe, I put any plant material that shows signs of disease in the city yard waste rather than my own compost bin.

cover crops

Cover crops hairy vetch and winter rye grow in a community garden plot.

So, yes—clean your vegetable garden out after or a frost or when you’re done harvesting the frost-hardy kales, brussels sprouts and leeks. If you clean out any areas by the end of September, you will have time (in zones 4 or 5) to quickly grow a cover crop that could be turned over in the spring. My favorite cover crop for my vegetable garden is a mix of hairy vetch and winter rye from High Mowing Seeds, but there are many options out there.

Another great inexpensive soil builder is to find a friend with a chicken coop—if they clean it out in the fall, offer to take away the old bedding straw. It will be high in nitrogen and carbon, so if you spread it out after you remove your plants, it can compost in place over the winter and be turned in come spring. Be aware of wind direction while doing this work because it doesn’t smell the greatest.

I also grow comfrey as a soil amendment. There are many online tutorials of the various things you can do with comfrey, like make compost tea or add it in layers to your compost bin, but I often simply pull the leaves and lay them on top of the soil. They break down by spring. It’s another easy way to add nutrients and organic matter to your vegetable garden.

comfrey leaves

High in nutrients, comfrey leaves can be spread out on the vegetable garden and will compost in place.

So now that we have some ideas for overwintering our vegetable gardens, let’s talk about perennials. There is a ton of value in leaving perennial flower areas of your yard unkempt for the winter. Seed heads of plants like purple coneflowers not only look fabulous in the snow, but they provide a food source for birds. Many of our native bees, moths, and butterflies overwinter in stems of plants like Joe-Pye weed or under piles of plant debris.

So, there you go! Clean up your vegetable garden, sow a cover crop or put down a soil amendment and put up your feet while we wait for our first frost to arrive. But leave some leaves and plant debris in your perennial beds—pollinators will thank you for it.


Purple dome asters pack a powerful fall punch.

Do you have some early fall gardening questions? Ask them in the comments below! We’ll check in and answer as many questions as we can for the rest of this week. If we don’t get to yours, you can Ask a Master Gardener via our online form, or call the Yard and Garden Line at (612) 301-7590.

Other helpful resources:
Yard & Garden Home
What’s wrong with my plant?
What insect is this?
The Master Gardener Volunteer Program


Jennifer Rensenbrink is a University of Minnesota Extension Master Gardener for Hennepin County. She grows native plants, vegetables and fruit in her south Minneapolis yard. You can follow her gardening adventures on Instagram.

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  1. Dianna Dunn on September 25, 2022 at 3:14 am

    I had gotten some peonies from my daughter in law abs rinsed down to roots. Put in fresh clean soil. Watered appropriately. And a 2-3 weeks ago powder donkey moms appeared on the leaves. I sprayed with copper solution but the white pieces still existed. Cut down stems and leaves. My question is; is it safe to transplant into my new garden beds or should I put in yardwaste. .

    • Jennifer on September 25, 2022 at 4:44 pm

      It is safe to transplant these into your garden! Peonies get powdery mildew nearly every year, and although it’s unsightly it doesn’t cause any harm to the plant.

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