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How To Make Fermented Salsa

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Wellness Mama » Blog » Recipes » How To Make Fermented Salsa

Now that we’re on the verge of tomato and pepper season, I wanted to share this recipe for fermented salsa. Fermenting fresh salsa is an easy way to make it last longer without canning and it adds a probiotic boost. Try it on tacos or with some homemade tortilla chips!

We eat and drink a lot of fermented foods, from water kefir to sourdough, to sauerkraut. Fermented salsa is definitely one of the easiest ways to get the health benefits of fermented foods in your diet. The fermentation process creates good bacteria that help improve gut health and the immune system.

If done properly, fermented salsa will last months in the fridge or cold storage and get more probiotics with age. This spicy Mexican condiment is a staple in our house!

Salsa Ingredients and Substitutions

While I like a little kick to my salsa, you can make this as mild or spicy as you like. For a mild version (especially for kids who don’t like spicy) use bell peppers. I’ll often grab whatever is ripe in our garden. You can also add jalapeno peppers, habanero peppers, or a blend of whatever you like.

The fresh tomatoes are really what makes this recipe so good though. If you don’t have any growing in your garden then check out your local farmer’s market. Homegrown and local is so much better than what’s available at most grocery stores!

I also included different spices in the recipe, but I don’t use exact amounts. Feel free to use however much of which spices your family likes. Or keep it simple and omit them altogether.

Whey vs Salt Fermentation Method

I usually make this with the whey leftover from making homemade yogurt cheese. This lacto-fermented version features beneficial bacteria from the lactic acid in yogurt, but it’s optional. You’ll still get probiotic benefits from just using salt. Fermenting the salsa also extends the shelf life.

If you don’t have whey from strained yogurt, you can also use some whey starter instead. Cultures For Health is a great place to get some.

Tip For Fermenting Salsa

If this is your first time fermenting veggies, there are a few things to know before you get started. Be sure to use a completely clean jar, lid, and supplies when making this. You don’t want to introduce any competing bad bacteria into your salsa!

Once everything has been chopped and mixed it will sit on the counter at room temperature for about 2 days. If your home is warmer (hello summer!) this process won’t take as long. You want to watch for fizzy little bubbles which will tell you the salsa is ready.

You don’t need any fancy equipment, but I prefer to use a fermentation weight for this. It keeps the veggies under the liquid so they don’t start to mold. If your salsa gets really fizzy you may need to “burp” your mason jar. Simply remove the lid to let some of the excess gas escape and then put it back on. Some people prefer to use an airlock or fermentation lid for this (to prevent jar explosions!).

How to Use Fermented Salsa

You probably already have plenty of foods your family loves with salsa, but here are a few of my favorite ways to use it!


Fermented Salsa Recipe

Homemade salsa with a probiotic twist; naturally fermented to add extra nutrients and flavor.
Prep Time 20 minutes
Fermentation Time 2 days
Total Time 2 days 20 minutes
Calories 18kcal
Author Katie Wells


25 servings


  • 3 lbs fresh tomatoes (about 4 and 1/2 cups chopped)
  • 2 peppers (such as bell pepper, cayenne, or jalapeno peppers)
  • 1-2 onions (about 1 cup chopped)
  • 4 cloves garlic
  • ½ cup fresh cilantro
  • 1 lemon (juiced)
  • 1 lime (juiced)
  • 2 TBSP sea salt
  • spices to taste (such as oregano, black pepper, cumin, chili powder, and cayenne pepper)
  • ½ cup whey (optional)


  • Chop tomatoes, onion, pepper, garlic, and cilantro and add to a large bowl.
  • Add lemon and lime juice juice, sea salt, and spices to taste.
  • Add whey (if using) and stir well.
  • Transfer the diced veggie mixture to a tall mason jar/fermentation jar. Pour in any juice from the bowl.
  • Press down to submerge veggies and place a weight on top to keep them submerged.
  • Seal the top of the jar and let ferment for about 2 days away from direct sunlight. It will get fizzy and start to get small bubbles.
  • After 2 days, remove the fermentation weight and enjoy or store it in the fridge.


Nutrition Facts
Fermented Salsa Recipe
Amount Per Serving (1 serving)
Calories 18 Calories from Fat 2
% Daily Value*
Fat 0.2g0%
Saturated Fat 0.03g0%
Polyunsaturated Fat 0.1g
Monounsaturated Fat 0.02g
Sodium 562mg24%
Potassium 171mg5%
Carbohydrates 4g1%
Fiber 1g4%
Sugar 2g2%
Protein 1g2%
Vitamin A 513IU10%
Vitamin C 19mg23%
Calcium 12mg1%
Iron 0.3mg2%
* Percent Daily Values are based on a 2000 calorie diet.


  • If you want a less chunky salsa then you may want to pulse it in a food processor before moving it into a mason jar/fermentation jar.
  • The exact fermentation time depends on how warm your home is. Fermented vegetables ferment faster in warmer weather.
  •  One serving size is about 1/4 cup.

Like this recipe? Check out my new cookbook, or get all my recipes (over 500!) in a personalized weekly meal planner here!

A Fast and Easy Tip

If you don’t have the time or ingredients to make your own salsa, you can get the benefits of fermented salsa by fermenting store-bought salsa as well. If possible, use the freshly made salsas in the refrigerated section, but you can ferment canned versions also.

More Fermented Food Recipes

Want to try your hand at more fermented foods? Here are some ideas to get you started!

Have you ever fermented veggies before? What’s your favorite way to use salsa? Leave a comment and let us know!

Katie Wells Avatar

About Katie Wells

Katie Wells, CTNC, MCHC, Founder of Wellness Mama and Co-founder of Wellnesse, has a background in research, journalism, and nutrition. As a mom of six, she turned to research and took health into her own hands to find answers to her health problems. WellnessMama.com is the culmination of her thousands of hours of research and all posts are medically reviewed and verified by the Wellness Mama research team. Katie is also the author of the bestselling books The Wellness Mama Cookbook and The Wellness Mama 5-Step Lifestyle Detox.


87 responses to “How To Make Fermented Salsa”

  1. Kelly Avatar

    I’m allergic to garlic, is the garlic just for flavor in this recipe? Or is it an important ingredient for the fermentation process?

  2. Sarah Avatar

    I made the salsa omitting the whey and only using 2 TBS of ses salt. After two days they didn’t seem to be any signs of fermenting. There were no bubbles, no pressure, nothing. I opened the salsa and everything looked and smelled fine though. We all ate a little bit of the salsa today, but now I’m slightly concerned and any botulism that could have possibly formed. Is there any chance of this or am I just letting my mind wonder too much? Thank you!

  3. Joe Avatar

    I’ve not used whey in recipes before. Can I used unflavoured whey powder supplement or is that different from whey starter? Thanks

  4. Rachel Avatar

    Hi, I am trying you’re recipe and want to know if powdered whey protein is acceptable? Will it work for the fermentation process?

  5. Zalina Avatar

    Hi! Can’t wait to try this recipe! Could you please tell me how cold should the cold storage be? I would like to make a large batch of salsa. I do have a basement and it is not heated but I wouldn’t describe it as cold either (in the summer anyway). It’s pretty chilly in the winter (Upstate NY).

  6. Melissa Avatar

    I have never fermented anything before, so I have a couple of questions. How do I know its fermenting, and how long does this process take, once it has fermented and I move it to my mud cellar or fridge, how long does the stay good?

  7. Morgan Avatar

    I’m trying your fermented salsa recipe, but need some clarification.
    It says: 6.Pour into quart of half gallon size mason jars…
    Does that mean put a quart into a half gallon size jar, or was it
    a typo and should have said “quart OR half gallon”?
    I went ahead and bought half gallon jars, filled them with 1 quart (half way),
    leaving them half empty(half full of air). Is that the point, or am I mis-reading it?

  8. Sarah Avatar

    Could I use this same method with the giardineira recipe that I already have, and just use the same ratio of salsa:whey?

  9. Rebecca Avatar

    I just made this for the first time. It is extremely salty. Is the amount of salt your preference or recommended for fermentation? Thanks!

  10. michele Avatar

    Since I do not do dairy, couldn’t you in essence just make a parsley bug the same way a ginger bug is made? This way I could make fermented salsa without the daily issues. Thank you!

  11. Alex Avatar

    As tasty as this sounds, I am very concerned with the safety aspect of this salsa from my food safety training as a food science student. Even though whey is being added, not all sources supply the live and active cultures that are necessary for lactic acid fermentation. The biggest concern for me is the placement of the salsa in air-tight containers with uncontrolled fermentation as well as an unbalanced acid profile from the “add what you want” nature of this recipie. This can create a perfect breeding ground for Clostridium botulinum bacteria that produces a lethal neurotoxin (botulinum toxin). I have included some very useful information and link from the USDA about safe homemade salsa production.

    Salsas are mixtures of low-acid foods, such as onions and peppers, with acid foods, such as tomatoes. It is important that ingredients are carefully measured and that the salsas be made as described to be processed safel, usually in a boiling water canner.


    The acid ingredients help preserve canned salsas. You must add the acid to these salsas
    processed in a boiling water canner because the natural acidity of the mixture without it may
    not be high enough. The acids are usually commercially bottled lemon juice or vinegar so
    the acidity level will be standardized. Use only vinegar that is at least 5% acidity; do not use
    homemade vinegar or fresh squeezed lemon juice because the acidity can vary and will be
    The amounts of vinegar or lemon juice in these recipes cannot be reduced for safe boiling water canning. Sugar can be used to offset the tartness of the acid. An equal amount of bottled lemon juice may be substituted for vinegar in recipes, but do not substitute vinegar for lemon juice. This substitution will result in a less acid and potentially unsafe canned salsa.


    Peppers range from mild to scorching in taste. It is this “heat” factor that makes many salsa fans want to experiment with recipes. Use only high quality peppers, unblemished and free of decay. You may substitute one type of pepper for another, including bell peppers (mild) for some or all of the chiles. Canned chiles may be used in place of fresh. However, do not increase the total amount (pounds or cups) of peppers in any recipe. Do not substitute the same number of whole peppers of a large size for the number of peppers of a smaller size (for example, do not use 6 bell peppers or long chiles in place of 6 jalapeños or serranos). This will result in changing the final acidity of the mixture and potentially unsafe salsa.

    1. Charzie Avatar

      I’ve read in numerous forums that there are no (lethal?) documented cases of food poisoning from lacto-fermentation. Plenty from canning, however. There were sources quoted but I didn’t check them out.

    2. CJ Avatar

      I think you may be confusing your food preservation methods. The above is true for canning of vegetables, but not for preservation using fermentation. With fermentation, abundant growth of lactobacillus will itself be acid -producing and these bacteria will outcompete other anaerobes such as clostridium.

  12. Tricia Avatar

    I’m trying this for the first time tonight. How much whey would I use for one mason jar? Are the lemon & lime juice necessary, or just for taste? Thanks!

  13. Earl Avatar

    I need a gallon of this salsa. Do I double it? Please advise.
    Thanks in advance.

  14. Sarah Johnston Avatar
    Sarah Johnston

    I have a couple of questions I plan on making some Fermented Salsa in the near future I was wondering Can I add Bell peppers to the recipe would it mess it up? Also Instead of using Whey since I do not have any I am going to use Sea Salt. The Sea Salt I have on hand is HAIN pure foods Seal salt will this work?

    1. Layla Avatar

      I am no expert at this, but I would think that adding the bell peppers would be fine. If the peppers are optional, then seems like bell peppers would be optional as well. Depending on how much you add, it might take it longer to ferment though.

  15. Emily Thomas Avatar
    Emily Thomas

    Hi there, just made a similar salsa…accidentally put too much whey, will that be a problem? And do all the veggies need to stay submerged somehow, or is it ok if they float?

  16. Sam Avatar

    I made some fermented salsa last night 🙂
    But today it is just sitting – nothing happening yet – when should I start to see it fermenting – i.e.., bubbles etc.????
    I made my own whey just by filtering the liquid from plain organic yogurt…..so it should be helping jumpstart the fermentation shouldn’t it?

  17. Jandan Avatar

    How do you know when your salsa is “done”? I have two jars on my counter that I made yesterday and was wondering when they need to go into the refrigerator. Thanks for all the great recipes! I used hatch chili peppers, which are in season right now in Texas, in my salsa.

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