Growing Onions – Problem with Rot?

A reader wrote to me about a problem she is having.  She writes: “Theresa, Have you ever had rotting onions about a month after transplant? I’ve noticed several that are rotten at the base, with no roots. They are slimy inside. Is this anything you’ve encountered before?”

Yes – and What I think It Is

Yes, I have had rotting onions — rotten at the base, no roots, slimy inside.

After 34 years of growing onions, I first remember encountering this about 3 years ago. (The onions had been in the ground 2 months rather than just 1 month.)  Although I try to keep gardening simple and not spend too much time trying to diagnose every and anything that doesn’t look just right, believe me — with 1,500 to 2,000 onions in the ground — I beat a path to my computer to try to find out what was wrong.

My best guess in naming the problem was (is) bacterial soft rot.

Shortly after that I received an email newsletter from one of the biggest conventional growers of onions in the country and they addressed this very problem.  According to them it is one of the most common onion diseases that their customers face.

As with any kind of  disease — you can find lots written about it and find lots of possible “solutions” which include chemicals.  This is when I pull back and think about what I know about my garden and what I want to do. My main focus is on good soil and garden health and that usually takes care of everything else.  But — I still had to do something.

What I Did

The first year I encountered the problem,

  • I checked my onions at least every other day. (Being on top of what’s happening is one of the most important things you can do.)
  • When I found an onion that didn’t look just right — I pulled it up.
  • All infected onions were taken off of my property in a plastic bag and discarded.

I may have lost 50 onions to this disease.

The second year I was on the look out and sure enough I again found this to be a problem.

I ordered a fungicide approved for use in organic gardens and sprayed my onions. Directions said to begin spraying two weeks after planting. My onions had already been in the ground two months. According to directions you are then to spray every 7 to 14 days through the growing season.    I sprayed only twice.

A reader commented below — why would anyone use a fungicide for a bacterial problem!? – Great question!

At the time I knew even less about disease problems than I know now. My garden is healthy so I never have gotten into diseases. And even though it would seem common sense that one could not “fix” a bacterial problem with a fungal spray – the spray I used was the organic spray recommended for what sounded like the same problem I was having.

The reader’s question certainly brings to mind that common sense can escape us even with the most obvious things. It certainly did me.

I don’t really remember, but I probably lost a few less than the prior year.

The third year (last year) I found some onions infected.  Not many.  I did not spray at all.

Keep in Mind

The pathogen or bacterium that causes this rot is in the soil and can be spread.  It can survive from year to year in the soil and crop debris. It enters the bulb through the neck tissue of plant and through damaged leaves.  Also insects can spread it.

Optimum temperatures for infection is said to be  between 68 and 86.  So just keep a watch on things.

As scary as all this sounds your main approach to any pathogen problem in the garden should be to do things that cause good health in the garden.  This will keep things under control.

Here are some other good gardening  practices that will help:

  • Rotate onion crops every 3 or 4 years.
  • Make sure there is good drainage where you plant.
  • If you water (I don’t) then avoid overhead watering (except rain of course).

Just a Gut Feeling

The second year I had problem with this rot disease, my mulch worked its way off my onions by harvest time.  That was in the middle of the worse drought I ever remember. The soil was like the desert.  Something deep inside of me was glad, because some how  even though every bit of organic matter was being oxidized — I felt the trade off was that the sun might be killing some of those pathogens. After the rains came in the fall, I started mulching and putting organic matter back into those beds.

Even though the next year seemed much improved, I’ll never know for sure if the sun killed most of the pathogens or not.  Especially since my onions are not in any one bed more than once every 3 or 4 years.

Final Thoughts

I have not sprayed this year and probably won’t until I see some indication of a problem.


Source for Fungicide Approved for use in Organic Gardens.

Other Posts on Onions

Onion Plants – A Bonus can be Green Onions in Winter

Onions – Why Grow A Lot?

Onions – Starting from Seed is Easy and Economical

Onion Sets – What You Need to Know to Get Better Results

Growing Onions

Bunching Onions – A Perennial Scallion Patch

Onions – More Reasons to Plant

How to Have Garden Onions April thru January

Onion Trivi


Organic Gardening is easy, efficient, effective and it’s a lot healthier.


All content including photos is copyright by TendingMyGarden.com.  All Rights Reserved.


  • We have some onions that are rotting from the inside out. Any ideas what could be causing that to happen and how to prevent it? Any suggestions would be greatly appreciated!

  • DeAnna, you’ve not given me enough information to really make a judgement. If your onions are already in storage and rotting, it could most likely be because they were not cured properly. See my post https://tendingmygarden.com/how-to-have-garden-onions-april-thru-january/

    If they are rotting in the ground it could be many causes. Your best prevention for all causes is good healthy soil, good air circulation, care in not damaging the onions, proper curing and handling.

  • A very interesting article and helpful, but although my onions (which have been in the ground for about 4 weeks now) are rotting at the bulb, the tops and the roots look really healthy. The only reason I pulled a few was to get some young onions for salad. I live in Manitoba, Canada and we are having a drought already, so don’t think over watering is the cause. Could this be a different problem, perhaps?

  • Carol, it doesn’t sound like the same thing based on what I’ve experienced. I’ve never had onion bulbs rot in the ground like you described.
    I’ve read that the root maggot can cause onion bulbs to rot. I’ve never had them and don’t know if that’s what your problem is or not.
    Overwatering can cause the problem as you already know from what you mentioned.

  • I have a problem with my onions rotting from the root up into the bulb. These are the onions that I will cure and then store for winter use! Any idea of what the problem might be!

  • Janis, the post you left the comment under answers your question “Any idea of what the problem might be?”
    It’s important to literally keep an eye on onions throughout the growing season. When you find you have a problem – take that onion (or onions) out immediately as I described in the post.
    Also as you probably already know, these onions won’t keep.
    Did you raise your onions from seed or purchase them?

  • For the last 7 or so years my onions start rotting in the garden. I have tried bulbs and I have tried green transplants. They look very nice, but when they are cut opened they are starting to rot in the middle. The centre looks good too. When we pull them out at the end of the season about one in four start rotting on the drying table. We lay them out single layer on a screened table. Good air circulation. Should I be soaked them with peroxide or giving them a vinegar rinse? Or what?

  • Debbie,
    For future reference, when you have a problem this serious, address it immediately rather than waiting.

    If this has been going on for 7 years I doubt it has anything to do with whether you plant bulbs or transplants.
    Peroxide and vinegar is not the solution.

    There can be many reasons for rot in onions.
    Overwatering (I don’t water at all.)
    Poor drainage.
    Poor air circulation.
    Onion maggot.
    To name a few.

    Once the pathogen (if it is that rather than onion maggots) that may cause this rot is introduced into your soil it can remain a long time.

    It is absolutely imperative to rotate a onion crops at least every 3 years ESPECIALLY if you’ve had any kind of problem.
    Also you can follow the other suggestions in the post.

    In order to TRY to determine the cause I need a LOT more information than what you gave.
    Do you garden organically?
    Does your soil drain well?
    Do you water and how often?
    Where do you source your onions?
    Have you/do you rotate your onion crops? How often do you rotate.
    Are the onions fully mature at harvest and do you see any sign of rot at harvest? (Some signs to look for are described in the post.)
    When did you first notice the problem?
    And other details no matter how small they may seem

    I would not plant any onions in those beds that you’ve grown onions in for at least 3 or 4 years.

    No matter what the problem is — you need to focus on good garden health and do everything towards that end.
    If you do that the problem may become manageable. Sorta like what I described in the post.
    If you read TMG on a regular basis you should know what good garden health involves.
    If you need more direction for that, let me know.


  • Joy, you can buy onions for transplants online or at your local farm supply company or
    The best transplants are the ones you start yourself from seed.

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