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. Plus it tastes delicious with some homemade tortilla chips!

Fermented Salsa Recipe
Ingredients
- 2½-3 lbs tomatoes
- 2 peppers (such as bell, cayenne, or habañero peppers)
- 1-2 onions
- 4 cloves garlic
- ½ cup fresh cilantro
- 1 lemon (juiced)
- 1 lime (juiced)
- 2 TBSP salt
- spices to taste (such as oregano, black pepper, cumin, chili powder, and cayenne pepper)
- ½ cup whey
Instructions
- Chop tomatoes, peppers, onion, garlic, and cilantro and place in a large bowl.
- Add the juice of the lemon and lime.
- Add salt and spices to taste.
- Add whey and stir well to incorporate.
- Pour into quart or half gallon size mason jars and cap tightly.
- Leave on the counter for approximately 2 days.
- Transfer to the refrigerator or cold storage (oh, I wish I had a cellar or basement!).
Notes
Nutrition
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?
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 🙂
Help can I use last year’s fermented peppers in my new salsa batch?
there r many tomatoes gng slightly over ripe or more in the markets..can I specially use them to make this fermented salsa?
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
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.
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
by saying whey do u mean normal WHEY ? LIKE THE ONE YOU BUY IN A PHARMACY? ???
making your own is much easier… powdered versions dont work well. easy to make though… https://wellnessmama.com/2402/how-to-make-whey/
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.
Actually fermented foods are beneficial for those battling candida. By adding fermented foods you are putting in good bacteria to crowd out the bad bacteria.
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.
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!!
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!
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 🙂