How To Make Fermented Salsa

Naturally Fermented Salsa Recipe

Now that we are just on the verge of Tomato and Pepper season, I wanted to share this recipe for cultured salsa. Fermenting salsa is an easy way to make it last longer without canning and it adds a probiotic boost.

We eat and drink a lot of fermented foods, from Water Kefir Soda to Sauerkraut, and fermented salsa is definitely one of the easiest ways to get the benefits of fermented foods in your diet.

If done properly, fermented salsa will last months in the fridge or in cold storage and get more probiotics with age.

Naturally Fermented Salsa Recipe

2 votes


How To Make Fermented Salsa



Yield 6 +

Homemade salsa with a probiotic twist- naturally lactofermented to add extra nutrients and flavor.


  • 2.5-3 lbs of tomatoes of choice
  • 1-2 onions
  • 4 (or more) cloves of minced garlic
  • Fresh Cilantro to taste (I use 1/2 cup or more)
  • 1 lemon, juiced
  • 1 lime, juiced
  • 2 TBSP sea salt or celtic salt
  • Spices to taste (I use oregano, pepper, cumin, chili, and cayenne)
  • Peppers (sweet or spicy.. I use cayenne and habanero but sweet peppers work great too if you don't like spicy!)
  • 1/2 cup whey (make your own!)


  1. Chop tomatoes, peppers, onion and cilantro and mince garlic. If you have a food processor, your could definitely use it to speed up this step!
  2. Toss all ingredients into large bowl
  3. Add the juice of the lemon and lime
  4. Add salt and spices to taste
  5. Add whey and stir well to incorporate.
  6. Pour into quart of half gallon size mason jars and cap tightly.
  7. Leave on the counter for approximately 2 days.
  8. Transfer to fridge or cold storage (oh, I wish I had a cellar or basement!)

Courses Condiment

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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 fresh made salsas in the refrigerated section, but you can ferment canned versions also.

Is your kitchen a small scale chemistry lab like mine? Do jars of foods in various stages of fermentation clutter your counter as they do mine? What’s your favorite?

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Reader Comments

  1. I walked into my kitchen yesterday and it smelled like apple cider vinegar (from the kombucha brewing on the counter) and sour milk (cheese cloth dangling from my cabinet with clabbered milk dripping whey into a bowl below). I had to light a candle because I’m still acquiring these smells.
    Looks like I have a new recipe to try with my newly made whey once my garden starts producing 🙂 

  2. I’m moving into a new place with a basement soon…might have to try this! Salsa is one of my favorite foods–it’s so versatile, and this looks like a great way to keep fresh salsa for Ohio winters!

  3. My husband used to call the forgotten leftovers in the fridge my “science experiments”.  He doesn’t know what to think now.  Water kefir on one side of the kitchen, kombucha on the other side….  Now I need to make some whey to try this recipe.  🙂 We live in Texas so salsa is consumed year round!!

  4. I have a sensitivity to dairy. Is there a substitute for whey? Thanks!

    • I haven’t tried it but supposedly you can just add an extra TBSP of sea salt.

    • You can use liquid from fermented Sauerkraut to start it. or whey from soy yogurt. I make my own soy yogurt, so easy and fermented soy is really good for you. This whey has the bacteria that you need. It must be live sourkraut or kimchee and not pasturized.

    • Do you know exactly what you are sensitive to in dairy? Is it the lactose, casein, or whey in cow’s milk?
      Unfortunately, if you have a casein sensitivity, it is hard (near impossible) to get whey without casein coming through.
      Most people who have sensitivties to cow’s milk can do goat’s milk. There is some conflicting info on goat milk whey proteins, although it isn’t clearly known why. So, you could make your own whey from goat’s milk and try that.
      I DO know that my functional medicine MD told me that after going off all dairy for a while (1 yr to 18mos.) that I could try whey and use it if I could tolerate it.
      But, if you are battling candida, you do not (yet) want to incorporate fermented foods. Again, going off fermented foods (1yr. to 18mos.) as well as carbs, sugars, etc.
      If you try the goat’s milk whey, I would love to know how it went for you.
      Otherwise, I would try the extra salt.

    • Hi! Sure, you can just leave out the whey. In fact, my group just recently had a discussion about the pros and cons of adding whey to lacto ferments, and the majority seemed to favor not using it for a variety of reasons, but these are just opinions, and you know what they say about those! LOL! The upshot is the microbes responsible for fermentation are pretty much everywhere…on the food, and in the air, so though the various additives (natural or purchased cultures) may cause fermentation to begin quicker, it will still happen regardless. For me, that is the “magic”, yet another gift of nature. Good luck!

      And thank you Wellness Mama for the recipe, it was just what I needed!

    • I use kefir water as a replacement!

    • Just open a capsule of any probiotic and mix in. But its going to ferment with or without whey.Toby

    • I use sauerkraut juice whenever I don’t have any whey handy. I’m hoping it would work fir salsa, that’s what I’m going to use Saturday when I make our’s.

    • You don’t need whey. You can do it with just salt. Whey is never needed for fermenting foods such as salsa.

  5. by saying whey do u mean normal WHEY ? LIKE THE ONE YOU BUY IN A PHARMACY? ???

  6. excellent idea especially on the buying ready made store salsa and adding whey…
    i am trying to do my own kraut now…woooo, stinky! doing only sea salt and cabbage.

    • The natural bacteria is already on the cabbage and other vegies if you don’t cook them. There will be many kinds of good bacteria. The sea salt is only there to keep any mold from growing and protects the good bacteria from being invaded by bad. There will be yeasts present too naturally. It will bubble away for a few weeks and create kind of a vinegar that helps preserve things even more. When it is as you like, good to bottle it and refrigerate and it will keep then a long time.

      We used to keep our brine pickled veggies and fruits in the basement (cellar) over winter as it was not heated. Everyone did that to keep fruits and veggies over the winter on Canadian farms and many now do it because they love it although using vinegar now is cheap and quicker but doesn’t taste the same. Strangely there are soil bacteria present in the ferment that also give benefit to the body. Keep some of the liquid always to use as a starter for the next batch. You can a bit of this to any ferment to increase the types of good bacteria. A good book on this by Sandor Katz

  7. I don’t have access to whey, can water kefir be used instead? Also can I use parsely instead of cilantro? Looks like a good recipe!

    • I don’t think that water kefir would work… different bacteria. Do you have access to any kind of plain yogurt??

      • I’ve actually been told that whey or kombucha would work to ferment because it produces the same lactic acid that ferments.  It’s not the beginning bacteria, but the end result.  I’m giving fermented salsa a shot with my water kefir.  It has worked in baking to replace whey or milk kefir, so I imagine it will work well!

      • I’ve fermented pickles with water kefir and they were excellent! They turned out much more crisp.

  8. Good Morning, I have 3 orange trees bursting with fruit and I have been searching high and low for a natural, healthy, sugar free version of Orange Marmalade. Any suggestions???? Thanks

  9. there r many tomatoes gng slightly over ripe or more in the markets..can I specially use them to make this fermented salsa?

  10. I really love this idea as I am currently making my own cream cheese and also tzatziki sauce so I’ll a lot of whey handy.  I am very new to this way of eating, so I have maybe a silly question.  If you don’t do grains – what do you dip in your salsa??  

    • I mainly put it on eggs, stir frys, salads, etc 🙂

  11. can you just put everything in a blender? that’s usually how i make salsa. it’s more liquidy but it’s still yummy.

    • You can, it will ferment faster though, so watch it carefully…

      • Ooooo! Thanks for this tip cuz I blended everything too!

      • Hello, I really enjoy your blog. I have a jar of just about empty Bubbie ‘ s saurkraut, can I use this liquid to ferment veggies, if so, how?

  12. What exactly makes something “fermented”? Is it just simply adding whey or is there more to it?

    • They whey actually causes a reaction, creating beneficial bacteria. It can also be done with just salt, though it takes longer.

      • Actually the whey contains the bacteria you need to start of the fermentation.

        • The vegetables have the bacteria required. Some would argue that adding whey actually creates an unnatural balance during fermentation. I just use salt, never add whey, and stuff ferments for me just fine.

  13. Sometimes do you have a little mold to scrap off the top?

    • Sometimes, I’d take the whole layer off and put in the fridge at that point…

  14. Question for you: I plan on growing tomatoes this summer and making TONS of fermented salsa but for this winter I’d like to ferment the jarred salsa. I don’t have any whey around my kitchen. My question is….can I purchase whey at a health foods store to keep in the fridge to use for this purpose? Or do I need to buy store-bought yogurt and make my own? Sorry for my ignorance…new to this! 🙂

    • You can purchase vegetable started cultures from places like Cultures for Health or just strain yogurt to make your own…

    • Just skip the whey, it’s not necessary.

  15. Sandor Katz eats savory vegetable sour dough pancakes almost every day, and he regularly makes sauerkraut, yogurt and kefir. He says eating and preparing fermented foods has become a staple of his life. “At certain times my kitchen looks like a mad scientist zone.”

    His new book The Art Of Fermentation is a massive tome that could seem overwhelming to a novice, but he stresses that the basic process of fermentation is really very simple.

    Many of his books available Amazon or at your library [url=] click[/url]

    See him on Youtube [url=…0.0…1ac.2.c-0sKeT99-A]click[/url]

    • Sandor is the master! Highly recommend his books! He has quite a few free videos on Youtube also. They are just beginning to realize how tremendously important our gut bacteria are to all facets of our health and are even calling it our second brain! Fermented foods are really a necessity and such a better option than spending our hard earned dollars on off the shelf probiotics! You even get a bigger and better variety doing it yourself, along with food value, the necessary pre-biotics, and for me, the satisfaction of having created it!

  16. You can purchase vegetable starter culture from a place like Cultures for Health and store that or make your own from yogurt…

  17. Are fermented foods safe to have during pregnancy? I am in the first trimester…

    • I’d always ask your doc, but I make it a point to consume a lot of fermented foods while pregnant since baby inherits gut bacteria from mom during delivery so good gut bacteria is important!

  18. I made this and have a few questions… it tastes a bit sour is that normal with fermented salsa? I’ve never tried it before. The other question is that I used whey concentrate 1/2 a cup of powder is that the right quantity for the powdered concentrate.

    • A little sour is normal, but I”ve never used powdered, just the homemade whey drained from organic yogurt. Is it like a protein powder? If so, I don’t know if that will work, but I woudn’t think so…

  19. My house always smells like “something’s going bad” but it’s the fermentation at work. Fermenting daikon is particularly stinky. LOL Yes, there are weird jars of things sitting on my counter and in the fridge. I like to ferment just tomatoes and hot peppers (Thai chilis are my favorite right now). When ready, if I want salsa, I add some fresh cilantro, scallions, fresh lime juice and serve. Otherwise I eat as is with a some squeezes of lime and some black pepper. Versatile. So healthy and DARN, my batch won’t be ready for 2 more days!!! Everyone enjoy!

  20. This sounds simple and delish. Could you ferment the salsa with just sea salt and leave it out on the counter a little longer as you would sauerkraut?

    • Yes, I don’t add whey to my salsa. I move it to the fridge after 2 days still and then let it sit there for a while to ferment slowly, but my brother-in-law ferments his for a few weeks at room temp.

  21. 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.

    • I want to know this answer too!

  22. 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… it should be helping jumpstart the fermentation shouldn’t it?

  23. 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?

  24. 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?

    • 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.

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

  26. 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!

  27. 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.

    Link to USDA Guide:

    • 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.

    • 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.

  28. 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!

    • Sorry, dairy issues.

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

  30. Giardiniera is my favorite!

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

  32. 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?

    • Quart or half gallon works and you can fill close to the top

  33. 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?

  34. 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).

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

  36. Can I ferment my homecanned salsa that contains vinegar?

  37. Will this salsa be sour tasting like most fermented foods? Thanks

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

    • No, whey powder is different and will not cause fermentation.

  39. 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!

    • This recipe needs the whey. I would personally not use it without the whey for fermentation.

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

  41. Can I use powdered probiotics instead of whey?