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 where 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.


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