How do you get rid of fungus in the garden soil?

A fungus is something that almost any gardener hates. They not only look bad but also harms our garden. The fungus is the main source of root rot and blight in plants. So, do you know- how to get rid of the fungus in the garden soil?- If not then keep reading.

What is a Fungus? – It is very basic though let me explain it. A fungus is a group of organism better known for spore formation. Actually, any organism that produces spore and feed on the organic matter is somehow treated as fungus. It is neither a plant nor an Animal.

Technically all member of fungus is actually a eukaryotic organism and classified in the kingdom Fungi. They range from single cells like yeast or mold to multicellular Mushroom. I think you like that in your plate as I do.

How to Remove Fungus from the Garden Soil?

What causes fungus in soil?

Fungus loves the warm, dark and humid environment. Lots of moisture in a warm climate is the main cause of fungus growth in our garden. In fact, the darker parts of the garden face the most fungus outgrowth.

If it is a delicious button mushroom then, you may like it but else wise it is completely waste.

The excess of moisture and availability of nutrients in the soil is the prime concern for the fungus. Believe me or not, the fungus growth shows that your garden soil is very healthy and full of nutrients. The only problem is with the fungus, they can cause root rot. The main reason for plant death is certainly the root rot. So if you are planning for a beautiful flowering garden, then you should get rid of the fungus as soon as you can.

How do fungi affect the soil?

Fungus generally does not harm the soil itself. The only problem is with the deficiency of nutrients and the growth of excessive fungi can kill your loving plants. Some of the direct effect of fungi on the soil is-

  • Increase the water holding capacity of the soil.
  • Balance the mineral content in the soil.
  • Help in decaying the hardest of organic matter.
  • Excess of fungus will increase salinity in the soil.
  • Consumes nutrient faster than any plant.
  • Create dead patches in the soil, especially in the lawn. It seems like a deserted spot between the grass cover.

Is fungus always harmful to the soil?

For me, it is sometimes yes and sometimes not.  It is obvious to say that fungus is harmful, especially if you are a farmer. Other than that fungus is harmful to most of the flowering plants we grow. But on certain occasions, these are helpful also, especially if you would like to eat these.

Whenever there is a scarcity of moisture and you want to prevent the soil from over-drying. Then you can use some fungus moss to reduce evaporation. It is a very effective way of mulching and even used to give an authentic look to several bonsai plants.

How to prevent the growth of Fungus in the soil?

To prevent your garden from fungus, you should follow these steps carefully.

Step 1.

Stop fertilizing: – Excessive use of fertilizer is the main cause of quick fungal growth. Fertilizer can act as a source of nutrients for the fungal spores.

Step 2.

Properly dry and decompose the organic fertilizer. Use of organic fertilizers is best for your garden, but if it is not properly decomposed then it will increase fungal growth in the soil.

Other than that, further decomposition will reduce the nitrogen present in the soil- resulting in wilting of plants.

Step 3.

Stop Overwatering: – too much of water is the primary source of fungal growth. Water only when necessary, don’t overwater and never make the soil soggy.

How to remove Fungus from soil organically?

Before discussing the main question let me ask another one. Is it really necessary to remove fungus from the soil? – The answer is definitely yes. Though it depends on the conditions, still it is always recommended to get rid of these nasty little creatures.

If it is necessary then how to remove it effectively and efficiently? Ok, starting with the basics. If you are a hobby gardener then you can do it easily for your garden. You don’t even need any complex tools or costly fungicide. Just follow these steps to completely remove fungus from your garden.

Step 1.

Spot the place where you think fungus has attacked. Identifying the fungus affected area is the first important step to get rid of these.

Step 2.

Look out for fuzzy hair like grey-brown growth over the soil.  It should feel soft when touched and looks like dust over the contact area. These tiny creatures form soft velvet-like structure over the spot they acquire.

Step 3.

If fungus is on potting soil, then the best thing to do is just re-pot the plant with fresh clean and healthy soil. It quite easy, and even a school kid can do it perfectly. If you need help you can read the steps for this- step given below.

Step 4.

If the fungus has infested the garden soil then you have to do several things. First, clean the area and remove all the grass.

You may have to remove several nearby plants. This is a little tricky. Do this step carefully if you want to replant these- I don’t recommend them to uproot, Either just clean the area around the root or remove few lower leaves and branches- it will be enough initially.

Uproot any plant only if there is nothing else to do. This can kill the plant so always be careful.

Step 5.

Once the area is completely cleared, just tilt or turn the soil at least up to 2-3 inches deep. Tilting soil will increase airflow and helps the soil to dry evenly. It also stops further growth of fungus as they need moisture to grow.

This step is very important, even professional farmers and commercial gardeners recommend this. If the soil is too moist then turn it to more depth and remove any debris if found.

Step 6.

If you are a hobby gardener then doing all these steps will be enough for your garden. Just leave the soil tilted for a few days. It will dry soon and if you want you can turn it further again for better mixing.

Other than that, you can use some kitchen products to kill the fungus fast enough that can be observed easily.

Kitchen products that can kill fungus

  • Cinnamon Powder
  • Baking Soda
  • Turmeric powder
  • Neem oil
  • Clove oil
  • Garlic Paste
  • Liquid Dish wash with vegetable oil

How to Use Cinnamon powder to kill Fungus in the soil?

If you want to remove fungus from your garden soil or even pot soil then you can use cinnamon powder for this purpose. Cinnamon is a great naturally anti-fungal agent available in the market. It is also very cheap and easily available. Follow these steps to use Cinnamon in garden soil.

Step 1.

Take 2 spoons of finely grounded cinnamon powder. It will be enough for the soil of two pots or for an area of nearly 1 x 1 feet in the ground.

Step 2.

In pots, firstly spread one or two pinches of cinnamon over the inner wall.

Step 3.

Mix the rest of cinnamon with the soil. Mix the soil evenly and properly. Try to leave no blots or lumps of soil.

Step 4.

Leave the soil mix in direct sun for 2 days. Don’t add any water in the soil.

Step 5.

After 2 or 3 days fill the pots with this soil mix and use it for any plant you like.

Step 6.

For Garden soil, just sprinkle the cinnamon powder over the desired area and mix it thoroughly up to 3 inches deep. Nothing more to do.

Special tips: – Use of this technique after the monsoon or rainy season is always recommended. Other than that you can use cinnamon once every month to keep your garden soil clean from the fungus.

How to remove fungus using Baking Soda?

Step 1.

Mix 1 teaspoon of baking soda in 2 liter or clean water. Please use tap water, mineral water is not really needed. Actually please don’t waste drinking water.

Step 2.

After mixing it thoroughly, add few drops of cooking oil or any vegetable oil in the water. This will help the water to stick with plants and leaves easily.

Step 3.

Spray the mixture over the affected area.  Use a sprayer if possible. You can also use a spray bottle to spray the mixture of baking soda and water to the affected area in the garden.

Step 4.

You can also sprinkle half spoon baking soda over the soil and mix it thoroughly. Add some water to mix it completely.

Baking soda is very effective for the excessive outgrowth of fungus in the soil as well as over the small garden plants. It dissolves the soft velvet-like covering and kills the fungus instantly.

Using Baking soda for removing fungus from the soil is a better alternative than using cinnamon powder. Yet, I always recommend cinnamon powder than anything else.

Care: – Excessive use of baking soda can be harmful sometimes. It can reduce the acid content of the soil i.e., the true acidity of the soil. Many plants like acidic soil and too much baking soda can disturb this balance.

Tips: – Only use baking soda mixture over the plants and soil if necessary. Whenever you find excessive outgrowth of fungus or it seems out of control then only use a diluted mixture of baking soda.

Use Turmeric powder to remove fungus from the soil

Just like cinnamon, you can also use turmeric powder to kill fungus in garden soil. In fact, turmeric is good for the soil. It can kill many pest and insects along with bacteria and fungus spores.

Step 1.

Just sprinkle a pinch of turmeric powder over the affected area. This will be enough to remove fungus growth. It also prevents further growth of any fungi and even prevents plants from insect attack.

You can even use turmeric with cinnamon powder. It is not going to harm any plant so, don’t worry about the quantity. Just use little as much as a tablespoon, it will be enough for a single pot.

Step 2.

You can water the area after using turmeric powder. I usually leave the spot untouched for one day after using turmeric.

Generally, I’d like to water the plants the next day after utilizing turmeric powder.

How to get rid of fungus using Garlic paste with liquid soap and vegetable oil?

Step 1.

Take 8-10 pieces of garlic. If possible take fresh and clean garlic.

Step 2.

Make a paste of these garlic pieces. Always try to make a smooth paste and don’t use premade paste for this purpose. We are not going to eat it, this is for your plants to keep it simple.

Step 3.

After that mix it with water. The mixture can be used in two different ways. First, you can leave it for 4 days and then use. Second, boil the mixture for a few minutes and then use.

Step 4.

No matter whichever way you choose, you have to follow the next step carefully. You should mix a tablespoon of liquid dish wash and a few drops of vegetable oil with 2 liters of water. Dish wash will help the mixture to stick with the leaf and over the surface of the soil. The oil will kill the fungus and spores by stopping airflow to them.

Step 5.

This is the final step. Mix the liquid carefully and spray over the soil near roots and leaves. Use this liquid twice in a week. Once used, leave the plant and infected soil for 3 days to observe the effect of the mixture. On the fourth day use the mixture again, repeat these steps until no fungus is left behind. This is a trial and tested method of killing fungus effectively and of course organically.

Does neem oil kill fungus? – Yes, neem oil is very good for controlling fungus growth. We can use neem oil to remove fungus from garden soil. Actually, I use both neem oil and leaves to remove pest, fungus, and insects from the garden.

How to use Neem oil and Leaves to kill fungus in the garden?

Step 1.

Mix a few drops of neem oil with water and spray it to the infected plants and soil. Always careful with the quantity of neem oil used. Too much of it can burn the soft leaves, so be careful.

Step 2.

You can also use dried neem leaves to prevent fungal growth in the soil. Firstly, crush the completely dried neem leaves and mix it with the soil.

Step 3.

Leave the soil mix in direct sunlight for a few days. Turn the soil upside down every day or once in two days if possible. This will aerate and dry the soil completely.

You can also use Neem cake to reduce fungal growth along with dried leaves and neem oil. You can ask your local garden store for neem cake and neem oil or you can buy it on Amazon.

Does Clove oil kill fungus? – Clove oil is effective to control fungus but I personally don’t recommend it. The main reason is cost and intensity. Clove oil is very hot, in fact, it can burn your tongue if you try to taste it undiluted. So think of using it over soft tender leaves, I think a little carelessness can kill your plant easily. Therefore, only use Clove oil if you need it and know how much to use.  Else you should try the other options.

Does lime kill fungus? – Yes, definitely lime can kill fungus, even in the soil. You can use a few drops of lime juice with water to treat fungal growth. It is effective for most of the plants that love acidic soil. Other than that you should be careful as it is acidic and excess of it can also burn the leaves.

7 Best fungicide you can use in your garden

  1. MilStop Organic Foliar Fungicide
  3. Daconil Ultrex Turf Care Fungicide
  4. Growers Trust Non-Toxic, Biodegradable – Natural Fungicide
  5. Docket DF-Generic Daconil Ultrexx fungicide
  6. ITS Supply Fosetyl-Al 80 WDG Turf and Ornamental Fungicide
  7. Organocide Plant Doctor Systemic Fungicide
  8. For more Fungicide <–

Steps to use Inorganic Fungicide

  • Take a small amount of inorganic or commercial fungicide. You can use a spoon to measure.
  • Use only 1 teaspoon of fungicide and mix it with a gallon of water. Dilution of the commercial fungicide is very necessary. Never use high concentration as it may harm your plants.
  • pour a small amount of this mixture in the soil. Always keep some distance from the roots. Avoid direct contact with the roots if possible.’
  • You can also spray this mixture over the plants. But I personally don’t recommend spraying over flowers and fruit. We come in direct contact with these flowers and fruits, so, any fungicide left over can harm us as well.
  • If used fungicide over fruits or vegetable, then you must wash it carefully before consuming. The commercial fungicide contains several harmful and poisonous compounds. These compounds can harm us easily,  so always take care of the use.
  • You must cover your face and hand completely during the use of chemical fungicide. You can even use a face mask and plastic gloves to prevent direct contact with these chemical fungicides.
  • Personally, I never recommend chemical fungicide instead I use organic one that I have discussed earlier. Hope you like it.

I have tried my best to explain the solution for removing fungus from garden soil. I have personally tried most of them and believe me the organic techniques are my favorite. What do you think about fungicide? Which one would you try and If you do then please let me know the results? If possible take pictures and I can show it with others to better understand the topic.


Hi, My name is Sukant. I am an I.T professional. Gardening for me is not just a hobby, it's a way of living life with nature. My Ancestors were Commercial farmers: So I personally feel attached to the green. I am not an expert, I'm here only to share my gardening experiences. It's always Refreshing.

9 thoughts on “How do you get rid of fungus in the garden soil?

  1. Hey all you excellent gardener friends, would like your advice.
    All of our Kerria Japonica along our back wall had black spot on the stems. I cut it all down, dug it up, cut and pulled roots and bagged it for the dump.
    Now I ‘m wondering about the soil. I read where fungi can remain in the soil and in the remains for roots. So I took off the top layer with mulch, pine needles, bits of cut KErria and its roots and made a pile that can also get bagged and go to the dump.
    The soil is also full of tree roots from our Norway Spruce and Birch trees.
    I don’t want to do anything that might harm or weaken, change the soil ph, etc to those trees.
    Should I apply an antifungal to the soil where the Kerria was.
    There are a number of products available, any suggestions you can offer will be greatly appreciated.
    Happy spring gardening, aren’t we glad it’s a safe thing to do!
    Hope you guys are well and staying safe.
    Thanks, cheers!!!

    1. Hi Christopher,
      The black spots are fungal spores. It is harmful especially when the moisture content is high. And yes, the spores can live in soil for a few days or weeks. The best part of your query is, you have almost treated it successfully. Now about your final question- Yes, you should use some antifungal solutions. I have shared many of those in my post. Just dilute it as suggested by the manufacturer and everything will be fine. Don’t worry proper use of fungicide don’t change the ph rapidly. Even I use contact fungicide to protect my plants once every month. You can also let the soil dry for a few days before planting anything new. Avoid adding compost or anything organic for first few days of treatment. for anything else just leave a comment.

  2. need some advice. I grow a vegetable garden every year. my last two seasons have been difficult. my vegetables seem to have contracted some fungus or desease problems. it seems to show up in my tomatoes, peppers, squash, zucchini. the symptoms seem to be the skins of my vegetables become very hard and never seem to fully ripen. the plants start off great look beautiful but the fruits after awhile stop ripening and get hard skins. they also develop whitish yellowish spots. can anybody diagnose or help me with this problem. thanking anyone in advance

  3. I have seven very large (approx 3’x3’x3’ each) pots that I’ve been growing tomatoes and basil in for the last two years. This year all the tomatoes developed and fungal(?) disease that severely stunted the growth. The leaves are curled in and discolored, spotted etc. I’d like to continue to grow tomatoes in these pots next spring without having to replace all that soil. What should I do to fix the soil? Pots are in a full sun location in Portland, Oregon.

    1. Hi there,
      Don’t worry the fungal problem is very common with tomatoes and can be cured easily.
      There is no need to change the soil completely, Although this is the best option. You can add 2 tablespoons of any contact fungicide to the soil before planting in the next season.
      Or If you want a 100% solution then, take out all the soil from the pots. Dry in full sun for a day or two, then heat it in the microwave or just dry fry it for 10 minutes. Let it cool and then add some dry compost and refill the pots. That’s it, this is all you need to do.

  4. Hi there. I started a 4×8 raised bed in April and I think I made a few mistakes along the way. I didn’t seal the cedar, and I probably could have used rock drainage underneath it, instead of turning the grass over and covering it with garden fabric. I also used mulch in addition to raised-bed soil and a mix of top soil and compost with manure. I’ve also fertilized the garden bed two times, which I now see may have been overkill.

    I’m in the mid-atlantic and of course there has been A LOT of rain in addition to intense humidity, heat, & sun. Since mid-summer I’ve started to see a variety of fungi. White powder fungus, Little light brown buds that turn into thin stalks with greyish faned caps, birds nest, puffball fungus (or so I think, they might have all been stinkhorn eggs), octopus stink horn and I believe elegant stinkhorn. I remove them carefully whenever I see them, and I’ve used an organic fungicide (with neem oil) twice, cinnamon, and 50/50 water+distilled vinegar+a couple of drops of Dawn a couple of times. I’d say these treatments partially worked, but I’ve still I’ve lost plants, and clearly need to till the soil at the very least.

    I try to keep an eye out and make sure the fungi are dug out, but I worry that I’m going to have to do something drastic in a couple of weeks when the first frost hits. Any ideas? Do I need to bit the bullet, remove the soil, clean the cedar and seal it (I’d read sealing cedar wasn’t needed) , add the soil back (with mulch and infected soil removed), let it go fallow and then solarize the whole thing next summer?

    1. Hi there,
      This situation is very common with raised beds. Don’t worry there is nothing wrong with your soil mix or setup.
      The problem is with the excess of organic matter in the soil mix. This is probably the reason for all fungus and bugs.
      I think you have tried every possible treatment. You can try sealing the cedar in next season But it is not relevant for the fungal problems. Instead, You can let the soil mix dry on its own and balance the organic matter with some clean river or construction sand.
      100% treatment can only be achieved with complete dry frying of the soil, this is not economical with a raised bed. So don’t add any other fungicide or fertilizer. Avoid any watering. Let the soil dry and just turn the surface once every week. I hope this should be enough to solve the problem.
      Thanks and Happy Gardening.

  5. Hi, my name is Joanne Bory I have a question about my front garden soil it seems not right. I keep dig turn around the soil so often and every time I got a lot of small roots some quite big and long , that is what’s means and how can I get rid off these roots? Thank you and look forward to get your advice

    1. Hi Joanne,
      First of all welcome to garden bagan. Now The answer to your question- Ye, you can get rid of roots from the soil. But the important point is, why do you actually want that? In fact, roots whether big or small indicates the great health of the soil. These roots show that your garden is healthy for plants. Now if you want to control them, then keep digging and tilling the soil at least, twice a month. Else add some salt-based weed remover or weedicides to your garden soil. This will reduce the growth of many plants like grass and other herbs or shrubs. Ultimately you will have fewer roots to dig in from your garden. Reply back with your decision, and state if anything needs to be corrected. Enjoy Gardening.

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