Stop Garlic Rust Before It Starts (and What to Do If It’s Too Late)

Rust is a rampant fungal disease that infects the entire allium family, including garlic and onions. If left unchecked, the disease can result in smaller-than-usual bulbs and limited growth of a plant. Learn how to identify the spores as soon as they appear, and what you can do to save your crop.

Linda Ly
Grrr... garlic rust and how to deal

After a particularly rainy and dismal spring, followed by May Gray (the predecessor of June Gloom on the west coast), a small patch of my garlic plants started developing white and yellowish-orange flecks on their leaves.

The flecks intensified, spread to neighboring garlic plants, and soon were infecting entire leaves, causing some to wilt and die off early. I even had the disease consume an entire plant, but luckily, it was close to harvest time and the garlic bulb survived.

You may have seen this on other plants too: onions, leeks, shallots, chives and even corn, wheat, sugarcane, and lemongrass are all susceptible to this disease.

But in this post, we’ll be focusing on a type of rust that’s most commonly found in a home vegetable garden: garlic rust.

What is garlic rust?

Rust is a fungal disease that affects garlic, but can also invade other members of the allium family, including wild alliums and volunteer alliums.

The word rust actually pertains to a whole family of fungi that affects a wide range of plant species, and it’s one of the most dreaded and rampant fungal diseases in the garden.

Alliums are commonly affected by the spores of Puccinia allii, a relentless fungus that travels by wind and rain (as well as by overhead irrigation, like sprinklers, or hand-watering methods that cause water to splash onto neighboring plants). That means a rust infection in one part of the garden may affect garlic (or other alliums) in another part, making it a challenge to contain.

This isn’t always the case though. Research has found that different strains of rust seem to have different crop preferences within the same locales.

For example, a University of California study found that P. allii infected garlic, onion, and chives in the state, but not leek, elephant garlic, or shallot. Whereas in Great Britain, rust is more commonly associated with leeks.

Early signs of rust start as small white or yellow flecks that are easy to miss. As the fungus spreads, the flecks grow into oval or diamond-shaped orange spots.

Garlic rust

Over time, these spots become darker orange or black pustules (raised spots), indicating a reinfection of rust in the same season.

Garlic rust

A severe case of garlic rust, especially one that appears early in the season, causes leaves to yellow and wither and limits bulb development.

Rust is an obligate parasite; that is, it can only survive on living plant tissue (similar to mistletoe). It’s also autoecious, which means it completes its entire lifecycle on a single host. So while it feeds on its host, it does not kill it (the infected crop). It merely reduces plant vigor.

Rust completes several cycles of spore production in one growing season, and can either overwinter on volunteer crops or produce dormant spores that survive the winter and wait for new hosts to infect.

Is it safe to eat garlic with rust?

Garlic affected by rust is still edible (and tasty) and unless the infection was severe, you should get a decently sized bulb at harvest time. There’s no need to prematurely pick your garlic crop unless the entire plant is brown and dead. (Like dead dead, not “ready and ripe” dead.)

Read more: The Trick of Knowing When to Harvest Garlic

True story: I once had a garlic that was so badly infected, I had to cut off almost all its leaves to curb the spread. All that remained was a healthy green stalk and a bright green mohawk, both of which hung on for the next three weeks until harvest. What I found underneath the soil was an average-sized bulb.

Whether the bulb continued to develop after its drastic haircut, I can’t be sure—but there was no harm in leaving it in the ground.

Below is a comparison of a healthy head of garlic with only a slight case of rust in the middle of spring, versus a garlic that had been heavily infected over winter. The healthy garlic is the same size or even larger than my unaffected crop, while the infected garlic is noticeably smaller.

Comparison of garlic bulb with minor rust and bulb with severe rust

Though the stunted garlic produced fewer and smaller cloves, they were still firm and flavorful and looked no different (other than being mini-sized and rather cute—I found them to be the perfect size to toss whole into a roast).

Onion plants infected with rust typically form smaller bulbs as well, but are otherwise safe to eat (just discard the infected leaves before curing your onions). The same goes for leeks, which might develop thinner stems if the crop is heavily affected by the fungus.

Alliums that are grown primarily for their leaves, like green garlic, scallions, and chives, can only be eaten if the plants are harvested immediately once rust appears. At that early stage, any infected leaves can be discarded in the trash, and healthy, unblemished leaves can be used in the kitchen.

How to store garlic or onions with rust

If a garlic or onion crop is badly infected with rust at harvest time, the leaves should be cut off, leaving a half-inch to an inch of stem on the bulb to keep other fungi or bacteria from entering.

Discard the infected leaves in the trash or in your municipal yard waste can. (Don’t compost infected leaves unless you manage a proper hot compost pile that heats up to at least 140°F to kill pathogens.)

Once the rusted leaves are removed, continue the full curing process with your garlic and onions, and store them like normal.

Related: 7 Secrets to Harvesting, Curing, and Storing Onions

How to treat rust on plants organically

Unfortunately, there are no reliable controls for treating rust organically.

Homemade remedies (with mixed results) can be found online, but in all honesty, there’s not much an organic gardener can do once garlic rust sets in.

The only way to get rid of the fungus completely is by snipping off the leaves as soon as the first white or yellow spots start to appear. You’ll have the most success with this if you inspect your plants daily throughout winter and spring to catch the infection early.

Throw the infected leaves in the trash (not the compost bin), wash your hands and clothes, and disinfect your pruning shears to prevent the fungus from spreading to other plants.

Read next: DIY Tool Station: The Fastest Way to Clean Garden Tools

Even with the infected leaves removed, the garlic stalk should continue to photosynthesize and send energy down to the bulb.

Easy ways to reduce or prevent allium rust

You are pretty much at the mercy of the weather when it comes to allium rust, but there are a few things you can do to try to prevent it:

  • The fungus flourishes when the weather is cool, sunlight is low, and humidity is high. If you live in this type of climate or had a very wet/gray season, avoid watering your plants late in the day, and especially avoid watering the leaves if they won’t have a chance to dry out before evening.
  • Use drip irrigation to water only the root zone of your plants and minimize water drifts or splashes.
  • Grow your garlic and onions in the sunniest spot possible, and allow enough space between plants for air to circulate among the foliage.
  • Fertilize adequately, but not excessively. Over-application of nitrogen (which results in lush foliage growth) has been found to make allium plants more susceptible to rust infections.
  • Rotate your crops and do not grow garlic, onions, leeks, and other alliums in the same area where rust appeared in the previous three years on any allium crop.
  • If any part of your garden was severely infected with rust, remove and discard all volunteer alliums that pop up the following season.

Even if your crop is plagued by garlic rust this season, all is not lost—you can still use the cloves as seed garlic for next season. A study conducted by the University of California found that seed garlic taken from rust-infected plants did not cause rust in the resulting new crop.

Simply choose the largest cloves from the cream o’ the crop of your properly cured and stored garlic heads, and give it another go this year!

More posts you might find helpful:

This post updated from an article that originally appeared on July 11, 2011.

View the Web Story on treating garlic rust.


  1. San Juan Island Washington State. Month of May has been wetter than usual and not very warm or sunny. GARLIC RUST. First time. Have raised beds with about 50 heads each. June 1st. One bed infected fairly heavy. The neighboring bed (2’ away) has none. Planted Both October 20, 2023. Usually stop watering July 4th and harvest 2 weeks later. My Garlic ( German Red) has won Blue Ribbon 3 years running San Juan County fair. I’m going to trim the lower heavily affected leaves, and spray with an organic fungicide even though I read “nothing organic works”. Will monitor next couple weeks…no scapes yet. If Rust continues…I will early harvest infected plants and hope they don’t spread to the others. Will report the results.

  2. I have a patch of garlic that is heavily infected with rust. I have removed all scapes as they appeared and the plants are dying from the top down. Only the bottom one to two leaves on average are dying back so it will be a few more weeks before I would normally harvest. Bulbs haven’t divided much yet. Wondering do I harvest soon or just wait til dieback occurs from below enough to do usual harvest? Thanks so much!

    1. Did you also cut off all the infected parts of the leaves? If the plants are dying back normally, I’d wait until the usual harvest time. The bulbs might end up a little smaller, but it’ll give them time to divide.

  3. Garlic rust is airborne, remove all leaves with significant rust and then go ahead and spray with Azoxystrobin which is a safe systemic fungicide that is used in the garlic industry to protect against it.

  4. Lots of good information here – since I do alternate all my planting sites each year and clean up all the raised beds in the fall, is there anything else I could do once the beds are cleaned this fall…I want to plant more garlic bulbs to winter over and will choose a different spot, but worry that this rust disease can remain in the soil over winter. Thank you for any suggestions! We live in northern Wisconsin and had a very late spring this year but the summer months have been quite warm and humid. I was so sad to see my chives, garlic and onions all affected by this – first time ever.

    1. Garlic rust does not survive in the soil unless its black rust which is extremely late in the life cycle spray with fungicides before it gets to that stage and you should be okay

  5. Thank you.
    Very informative.
    Now I know what I did wrong this year. Too much fertilizer!
    Ready to do better in 2023.

  6. THIS is an excellent, clear discussion of what I’m seeing on my garlics this year, for the first time. Clear, plain writing is so rare these days that I want to commend you on anticipating all my questions about garlic rust and answering them. Brava!

    1. Thank you so much this is exactly what I’m seeing in my farm although watering is by drip.
      Now 20% of the crop is affected. And I’m left with 2 months to harvest my garlic , it looks like the Allium Rust is invading the whole crop especially in the leeward side.

  7. Just harvested and most of my plants had this. Bulbs are beautiful. If I need to cut all the leaves before curing, what’s the best way to cure without leaves?

  8. No problem composting rust infected leaves as the fungus is airborne and will rot in the compost bin over winter and not be alive in the soil from your compost the next year.

  9. Hello! Thank you for the info on red rust. It has infested our garden via the raspberries and torched the garlic in the process. I am wondering if soil solarization is required (or even useful in non-raised beds) before planting anything else, or will red rust only affect certain plants? I would like to plant tomatoes there, but want to make sure I’m not just spreading the rust infestation to new plants! Thanks!

    1. Soil solarization does not work on airborne diseases like rust. However, you can try to prevent future rust infestations by removing and disposing of all affected plants in the garden, since the spores can overwinter on certain perennials. For future plantings, be sure to allow enough room between your plants for air to circulate, avoid watering from overhead, and mulch your beds.

  10. I have a soft area at the base of garlic scapes and usually some brown spots. What is it and is there a cure

    1. Hi, it’s hard for me to say as I don’t know your growing conditions. But any soft/brown spots at the base of your scapes (which would be the top of the bulbs) sounds like there might be rotting. You’ll have to pull a couple of the bulbs and check.

  11. The rust on my garlic seems farther along than the rust in your pictures. The entire leaf of the garlic is covered with rust, even into the crevice where the leaf meets the stalk. When I cut off the leaf, there is still a strong patch of rust right in the crevice that is left. My garlic still has probably a month until maturation, do you still suggest just cutting the leaves as close to the stem as possible, or do I need to take more drastic measures?

    1. Sorry for the late response on this. But to answer your question for future reference, you have to remove all affected leaves completely, or harvest the garlic and eat it right away. Rust spreads by air or water, so leaving any remnants of it will only encourage it to spread to healthy plants. Immature garlic is edible and delicious; it just won’t cure and keep for long storage.

  12. My Garlic almost ready for harvest caught by rust. Now completely killed by rust. In the same area we planted maize, sag, and other vegetables and had the same problem. All the maize leaves before flowering turned to red, completely burned, soya bean burned down with rust . Now how can i treat this soil so that i can have rust free soil so that i can harvest my crops healthy. My email id is and also connect live on skype id birbdrwaiba123.

    1. Rotate your crops so that the rust-prone plants do not grow in the affected soil for at least 3 years. Bag and discard of all the infected plants. Disinfect your tools, gloves, gardening shoes, and any other items that have come in contact with those plants so as to not reinfect the next year’s crop. If the rust infection was widespread throughout your garden, you may want to consider solarizing your beds:

      1. What can I plant? I pulled my garlic today. I was lucky and have nice bulbs for the most part. But I would like to use the two spots where I had my garlic. Would like to plant something other than lettuce

        1. Fall crops you can plant include root vegetables, chard, kale, broccoli, cabbage, collard greens, peas, fava beans, parsley, cilantro, and dill… lots of options depending on what you like, how much sun you have, and whether you live in a zone with a hard freeze.

  13. Oh thank you for this… I was just about to harvest all my garlic early. I checked on one and it seems ok (and HUGE!) I’m on the west coast and one of my raised beds all have this rust, while two others nearby are (so far) free of it. Pretty sure I have the same soil… Also I’m wondering about curing the rust-garlic. The ones I dug up I cut off all greenery (orangery) and they are hanging in my storage room, but I think I’ll follow your advice and only cut off leaves and cure with just stem. Also, have you heard of solarizing your bed (covering completely with see through plastic) to kill off unwanted disease/seeds? Supposed to leave the good bacteria alone, but I’ve never tried it. I might try on this rust bed after harvesting.
    Thanks for your post!

  14. Very useful, Linda thanks. I live in England (it is really rainy at the moment) so conditions aren’t great but I think I can salvage it as it’ll be ready to pull up in a month or so. Really useful info on how to look at things for next year and so on. Thanks.

  15. thanks Betty, great post. Helpful, informative and thorough. Rust seems to come and go with damp seasons, cheers ben

  16. Thank-you so much Garden Betty!  Your info on garlic rust is exactly what i was looking for. Practical, and well written. I will take your advice.  Confidence is high!

  17. This year is not my year for gardening. Bad, bad garlic rust that we had to pull them out today and some of the cloves are really rotten :(. On top of that, my potatoes have blight so they too had to be pulled. Should I blame the Vancouver BC weather? I don’t know. It is so hard to be organic, grrr.

    1. Living on the coast, I also have difficult summer weather (misty mornings and evenings). I didn’t get garlic rust this year, but I made sure not to plant my new garlic or onions in the same beds. I’ve heard that blight will remain in the soil as well, so throw everything in the trash (plants, mulch) and leave the soil exposed so it can freeze over winter and kill the spores.

      1. Wet climates breed many fungal diseases. Try introducing good bacteria and fungi. I use Mycogrow from because it is a wide variety of organisms, but there are other products. I put it on the cloves when I plant, and spray it on the plants later. The rust is endemic to the blackberries that grow on my neighbors fence and so I spray them too. The blackberries look great as a result. I get black spots on my apple and pear trees, and it looks like the fungus that grows on the adjacent myrtles, so I spray them too. It’s not a 100% cure but it keeps the plants healthy and it’s not a chemical.

        1. Hi, I’ve only just found this, googling around for rust which I have always had on my leeks, garlic, welsh onions etc. I live in Brittany France and for the last three years we’ve had June Gloom and all that goes with it. I first looked at what the RHS (Royal Horticultural Society) had to say and its “rust occurs on nitrogen rich low potassium soils (btw comfrey is a great source of potassium so mulch with that) and that “Puccinia allii has been confirmed
          as being seed-borne, but this is not currently thought to be of any
          great significance in the spread of the disease.” Your blog is really informative and it’s interesting that the UC has found different results. I wonder what the RHS source of info is. I’ll ask!

          1. I haven’t had any rust the last two seasons, though we’ve also had unusually dry winters and springs. Does soil have a part in it? I’m not sure, as I didn’t do anything differently to amend it.

          2. I’ll try potassium. Greensand and comfrey. The red clay soil around here is very low in potassium and calcium. The fir trees and mushrooms like it but everybody who doesn’t add calcium gets blossom end rot. Composting kitchen scraps with the garden waste helps. We have been having the same dry winters, scary because if the rainforest gets dry enough to burn then we’re in big trouble. We get a lot of late spring rain when it is warmer and the fungus loves it. But then the rain has been starting later in the fall so we can get a few extra tomatoes, figs, and lots of blackberries. I get my little girls up early on Sat morning and take them out to pick blackberries so mom can sleep in. When mom calls us in for breakfast then she takes the blackberries and makes a pie crust out of brownies and butter, pour in the blackberries, cover with marshmallows, and stick it in the oven. When the marshmallows run together its done. Eat it early in the day so they can burn off the sugar.

          3. This is the 3rd year in a row planting garlic in the same spot. 1st year was awful due to rust and root rot. 2nd year was better using mycogrow. Last winter I dug greensand and oyster shells into the soil, used the mycogrow again, and had a great crop. I grow hard neck and had some heads almost 3″. Early rust outbreak was stopped by spraying mycogrow. I harvested early because I was afraid of the late rains and root rot, which did get maybe a dozen heads. I gave a bunch to friends and made up over 3 gallon bags of garlic ice cubes.

          4. Its not seed borne, its been confirmed that it doesnt live on or pass via seed route, only aerial from other crops that act as hosts in the wind

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