Fermented Salsa

This isn't just any old salsa. This is fermented salsa.

If you're like me, you love salsa. It's true, I grew up in Texas. But salsa isn't just for Texans anymore. Salsa is the number one condiment in America (mustard is number two).

What's fermented salsa, you ask? It means it's probiotic. Like yogurt or kefir. With all the assaults we have on our gut flora — from antibiotics to the birth control pill to chlorinated water — we need more probiotics.

And in summertime, when we have an abundance of tomatoes in our gardens, it's the perfect time to make salsa.

That's a picture of my dear step-father, and native Texan, Otter, chopping peppers. He's not wearing gloves. But he's a Texan — we're tough. (Plus, he has a special technique — look how clean his board is and how perfect those peppers are.) I recommend wearing the gloves.

Oh, and did I mention that because this salsa is fermented, it will keep in the fridge for weeks and even months on end?

Stay tuned. I'll be posting my recipe for tortilla chips fried in coconut oil soon.

Fermented Salsa

Fermented Salsa

  • Author: Ann Marie Michaels


  • Chili peppers (1-2 serranos or 1/2-1 jalapeno, depending on how hot you like it)
  • Medium fresh tomatoes (4), or canned tomatoes (1 pound), organic if possible
  • Medium white or yellow onion, organic if possible (1)
  • Garlic cloves (2)
  • Lemons or 3 limes, organic if possible (2)
  • Sea salt (1 TBS) or
  • whey (2 TBS) — if you don't have any whey, use an additional 1 tablespoon salt

Optional: 1 bunch oregano, fresh (or 1 teaspoon dried)
Optional: cilantro (1 bunch), fresh
Optional: Filtered water


1. Wearing gloves, cut open the chiles and discard the stems and seeds (If you don't wear gloves, you risk burns — trust me, I've done it. I advise wearing the gloves.) Set aside.

2. If using fresh tomatoes, peel and deseed them: Fill a large saucepan halfway with water, set on high heat and bring to a boil. Carefully set tomatoes in saucepan and let sit for 5-10 seconds, then remove with a slotted spoon or tongs. Cool and peel. Cut tomatoes in half and gently squeeze out the seeds, or scoop out with a spoon, and discard. Set aside.

3. Peel and quarter the onion and peel and smash or crush the garlic.

4. If using fresh herbs, rinse, dry and chop them, discarding the stems.

5. Place the peppers, tomatoes, onion, garlic, and optional herbs into the food processor (you can also do this by hand — just dice everything with a sharp knife).

6. Squeeze the 2 lemons or 3 limes and add the juice.

7. Add the sea salt and whey.

8. Pulse several times (more or less for desired consistency).

9. Transfer to quart-sized mason jar. Add a little filtered water if necessary (if you like it more liquid and it's too chunky). If you add water, put the lid on and shake it up so it's incorporated. Make sure to leave at least an inch of space from the top of the jar.

10. Cover and keep at room temperature for 2-3 days before transferring to the fridge. Salsa will keep for weeks or months in fridge.

Did you make this recipe?

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Equipment Needed for This Recipe

Rubber gloves
Quart-sized mason jar with lid
Optional: Food processor

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Fermented Salsa

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Ann Marie Michaels

I have 25 years of experience in digital and online media & marketing. I started my career in Silicon Valley and Los Angeles, working at some of the world’s top ad agencies. In 2007, after my first child was born, I started this little food blog which I grew to over 250K monthly unique website visitors and over 350K social media followers. For nearly 15 years, I've helped my audience of mostly moms and women 25-65 cook for their families and live a healthier lifestyle.

 The year after I started the blog, I founded a blog network in the health & wellness space called Village Green Network. I started the company on my coffee table and bootstrapped the business to over $1.3 million in annual revenue within 5 years. During that time, I helped a number of our bloggers become six figure earners. After being censored on almost every social media platform for telling the After being censored on almost every social media platform from Facebook and Instagram to Pinterest and Twitter, and being deplatformed on Google, I am now deployed as a digital soldier, writing almost exclusively about politics on my blog Cheeseslave.com. Because who can think about food when we are fighting the second revolutionary war and third world war? Don't worry, there will be more recipes one day. After the war is over.

106 thoughts on “Fermented Salsa

  1. What are other storage possibilities if you don’t have room in the fridge for a whole big bunch of salsa jars? Do you know if it is possible to ferment, then store in scalded jars?

  2. This is my 2 year old daughters favorite ferment! She could eat a whole jar of this in one sitting if I let her.

  3. Jennifer,

    No, I don’t think so. This is a living food.

    If you have cold storage, like a root cellar, that would work.

    What you could also do is make it in smaller batches. If you don’t have access to good local tomatoes in the winter, you can make sauerkraut in winter instead, and salsa in the summertime.

    You *might* be able to freeze salsa. Not in the jars, but you could put it in freezer bags. However I have never tried it so I have no idea if it would work.

      1. BTW, freezing will not kill the probiotics. They will go dormant while frozen but will reanimate once thawed. This is true for most fermented products including yogurt and sauerkraut.

  4. Hi there,Newbie Lynn here.I am def going to try this,it looks delish.At the moment have got cabbag with red beetroot ,,and spanish melon peel with cinnamon ,,as well as chillies,garlic and ginger,fermenting.Tomorrow am going to do my Kimchi.Am addicted to ferments!oh also got sough dough starter on the make,and of course my K.T. and Kefir-both milk and applejuice Kefir.
    I love the look of the site,and will be trying loads of your recipies.Thank you.Lynn

  5. My three year old could live on salsa I’m convinced. It’s her condiment of choice for sure! I was just looking at the pile of jalapenos on the counter wonder what to do… now I know! Thanks!
    .-= .ambre.´s last blog ..Surf And Turf =-.

  6. Hi AnnMarie,

    This will be my first time fermenting vegetables.
    I’m going to try this recipe for salsa.
    In the book Nourishing Traditions, the instructions for fermented garlic have you bake the garlic at 300 degrees until the heads open up.
    That bothers me because you’re killing, at least, the enzymes.
    I see that you don’t bake the garlic before processing.
    Is baking garlic not always required for fermentation?

    Thank you.


  7. We LOVE this salsa and just pulled some out of the downstairs fridge that we made last year and the flavor is amazing.
    I was wondering, now that I’ve been fermenting awhile, would it be better to begin ordering some cultures to increase the variety of organisms in my fermented food?
    I mean, how varied are the micro organisms if I’m using the same whey for all of my ferments? Know what I mean?

  8. YES, that’s about how we like it too, with the cilantro of course! We also like it made with a little red or green onion thrown in.
    Why do you remove the seeds and membrane though? We use everything but the stem.
    Word of advice from another one who does not wear gloves for prepping: if you choose bare hands, DO wash them well with a generous amount of soap, even dish soap, immediately after and remember to keep your fingers away from your eyes, even after you have washed your hands!
    @Jennifer: you CAN freeze stuff in jars. I don’t know about the texture of this salsa after freezing but if you decide to freeze it use only wide mouth jars and leave about an inch and a half headspace to allow for expansion.

  9. You could freeze salsa, but it would be better if you blend it later to get more of a picante texture. (Tomatoes get mushy after defrosting.)

  10. Thanks for the recipe–I appreciate the fact that I could also use canned tomatoes–great for winter batches of salsa!

    1. Something almost no one knows… Many, if not most good Salsa’s are made from canned tomatoes! Really! Fresh tomatoes have too much liquid and spoil any recipe where they are not cooked down to eliminate their natural occurring water which helps them to “beef-up” their real tomato flavor.

        1. Brandy, she was not suggesting you cook the tomatoes just put them in boiling water for a moment so they are easier to peel.

  11. Wear gloves!! I recall 2 times of going to bed with wet washcloths wrapped around my hands after cutting hot peppers. You would have thought once would have been enough! Can whey from kefir cheese be used for the fermenting?

  12. I love my salsa this way too! It’s way better than even just fresh salsa, at least to me. You really can take any salsa recipe you already like and turn it into a lacto-fermented one! I even made lacto fermented gazpacho -yummy! which is nice because it lasts so much longer that way!

    My recipe is similar – here;


    and one for Smoky peach salsa, here;

    .-= lydia´s last blog ..Ginger Vinaigrette =-.

  13. Outstanding recipe, Ann Marie! Gloves…..LOL…..woman, I’m Bulgarian! I’ve been peeling roasted hot peppers since I was 4! The only thing I can do with gloves on is to clean and wash stinging nettles before cooking them! That’s another season, though. P.S. Flat-leaf italian parsley is also a good option in place of the cilantro.
    .-= Val´s last blog .. =-.

  14. I learned how to handle jalapenos peppers from a restaurant magazine. Cut the pointy tip off. Cut the stem end off. Stand on the broader end (where the stem was) while steadying with your thumb and pointer finger holding the narrower end. Cut small sections downward, just skirting the seeds. You will have a nice bunch of pepper strips and the seeds will pretty much be left hanging onto the pithy center of the pepper. No burning fingers this way. Just don’t rub your eyes! I’m looking forward to doing this recipe with fresh tomatoes–loved the canned tomato version last winter.

  15. Sorry this is a little off the topic, although the salsa looks interesting to try; I’ve just made my first jar of lacto-fermented cucumber slices and my first-ever jar of sauerkraut is currently downstairs doing it’s business!

    Anyway, I just got hung up on the mention of the birth control pill. If there is anybody that is interested enough in food and being healthy to read and comment on your blog they should really think twice and then about five more times before putting that stuff in their bodies. (The havoc it wreaks on your gut isn’t even the half of it.)

    Believe it or not, there are healthy, “green” ways of not getting pregnant (and for getting pregnant, for that matter) that really do work and really are effective. All it takes is learning more about your body, understanding it’s signs, and then putting that information to use.

    It’s called the Creighton Model FertilityCare System. Learn more:
    .-= Diane´s last blog ..You might be a health nut if =-.

  16. AnneMarie!
    I am so excited to try the salsa for the first time! I made a big mess but it smells and looks delicious. I used red peppers. When I added everything it did not fill the quart jar is that allright? I did not want to add water because I liked the consistancy the way it was. I had whey from raw milk—I hope it works because I cut it in half for one quart of salsa instead of two! Thanks for going over it so that I was ready to take a chance!

  17. I just made this salsa and noticed when I opened for the first time a slightly whitish color on the top. Is that normal? I stirred it up and it tasted great, but was concerned about this. Please let me know. Thanks.

  18. Lemon…. lemon???! Heresy!!! Salsa=liiiiiiiime, and cilantro not optional! But, teasing aside, this is a really great recipe and one I am going to make as soon as possible! It’s hard to get the lacto-fermented stuff in when you don’t like sauerkraut… or beet kvass… LOL. One day, one day!

  19. I am definitely going to make this this year! Thanks so much for sharing the recipe. Your salsa looks divine, AnnMarie. I can’t wait to try it and I’ll have to save some for my son who just moved into college last Thursday – he loves salsa.

    P.S. It’s so wonderful to get to see your step-dad prepping the jalapenos. Fun!

  20. I love to cook and I love salsa. I have never canned/jarred salsa before I usually just make enough to eat right at the moment. I make all kinds and I have never in my wildest dreams thought about adding whey protein. I was a whey protein junkie when I was training in competition fencing. I will give this recipe a sincere go this coming weekend. I just got my hand on some Mole’ chili peppers and I will add them into this as well.
    Thanks for this great recipe,


  21. Richard – It is NOT whey protein. It is real whey, which comes from yogurt or milk.

    See my recipe here:


  22. I made a double batch of this recipe today. It’s my first time making anything lacto-fermented. I could’ve used more tomatoes because I came up short of two quarts and didn’t want to add water, as the consistency looked good.

    Thanks for sharing your recipe, I’m looking foward to it!

  23. We love this recipe! And it is the thing that has saved my 7 year-old daughter from chronic constipation (and the magic of Dr. Tom Cowan!). My question is whether the removal of skin and seeds from the tomatoes is just for reason of appearance in the finished product or a more important reason? I’ve made it both ways and can’t tell a difference except that I’m much happier with that many fewer steps!

  24. Made a big batch of this salsa last week for the football games on Saturday. Love homemade salsa and glad this can last for weeks in the fridge. But someone mentioned they had a bottle from last year? Will it really last that long?

    I made the recipe as described but for us it was WAY too lime-y. I think next time I’ll only add one lime, and 1/2 a bunch of cilantro. A full bunch seemed to overpower the tomato taste.

    Also, when I left the salsa out on the counter to “lacto-ferment” for 2 days the cilantro turned brown. Did that happen for anyone else? Did I do something wrong? I made my own whey from instructions on this site. Thanks!

  25. Emily — I think the longest I had my salsa was maybe 9 months or so. After a while it starts to taste, well, fermented.

    As far as the amount of lime to add, I’m always loathe to list specific amounts in recipes like this one because everyone is different and we all like different flavors.

    I have not had the cilantro turn brown… but maybe I never noticed It should all just meld into the salsa. I wouldn’t worry about it if it tastes good.

    That photo was taken BEFORE it was fermented, by the way.

    1. I did, and it’s excellent! We had a mishap with green tomatoes when my daughter tipped over our earthbox. It was the perfect save for them! Afterwards, I mixed the salsa with roasted corn…yum!

  26. Wow! I just tasted my first batch and I will never eat any other salsa! This stuff is amazing and definitely my favorite lacto-fermented food by far. Thanks so much for the great recipe!

  27. This looks amazing! My family’s favorite chicken recipe is a bunch of leg quarters tossed in a crockpot on low all day, with a couple jars of salsa poured over it. Then use tongs to pull out the bones and gristle while shredding the chicken. Use in tacos, enchiladas, or just spoon over broken chips for chicken tortilla soup.

  28. Hi! I made this for the first time, and I had a question… I let the salsa ferment for about 3 days before tasting, then placing in the fridge. It was pretty good, but I left 1 jar out to sit a little longer since it’s so cool in my kitchen (there is no radiator in my kitchen, and it’s averaging around 40 during the day). The jar I let sit for another day and a half, I just opened today and it was sooo much better! Would it be OK to pull the other jars I’ve had in the fridge out to re-ferment for a few more days? Or will that make them go mouldy/sour? Thanks!!

    1. woops- I see the recipe actually has the whey measurement. Sorry! Anyway I made it with the salt last week and it was FABULOUS! THanks!

  29. tried this a while back with the extra salt bc I didn’t have whey and couldn’t eat it due to the saltiness but tried again this week now that I had some whey and its fantastic!!

  30. That’s crazy that salsa is the number one condiment! I would have definitely thought it was ketchup… I have yet to make fermented salsa I am happy with. I will try again when the tomatoes are ripe!

  31. Ok, today is day 3 and I have some fuzzies growing on the surface of 2 of my jars….is it ruined?? Can I just skim it off and call it good? I don’t want to get sick 🙁 Going to open the jars after work today.

    1. Ok I think I found my answer elsewhere…apparently it was kahm yeast which is very common if you aren’t using a harsch crock and is harmless. Just skim it off as best as you can. It has a very distinctive look compared to mold (you can find pics if you google it)

  32. Hi,

    Can the juice left-over from making the salsa be used for the next batch of salsa instead of using whey?

  33. I tried your recipe for the first time today. Can’t wait to try it in a couple of days! This is my first venture into fermentation!!

  34. Hi,
    This looked so good. Made a batch with homegrown tomatoes and jalapenos. BUT after 3 days on top of fridge it has grown MOLD – yucky grey black fuzzy stuff. I put the salsa in a mason jar with the lid screwed loosely on.

    Should I have put it somewhere dark? Should I have put it in the fridge a day sooner? (It’s summer here in LA – warm but not crazy hot.) Was it something else??

    Any tips appreciated. I’d like to try this again.
    (PS. I don’t think this is the kind of mold you scrape off and eat under….)

    1. Liz,
      I am no expert, but I have made 3 successful batches of this salsa recently. I used Mason jars but I screwed on the lids tightly and once a day I would loosen them just enough so that built up gas could escape (there was always an audible hiss). 2 of my batches grew kahm yeast, which is very different looking than mold. From what I have read, if it is any color other than white/beige then it is likely mold and not worth the risk. Kahm yeast is white and bubbly (there are pics if you google it).

      I left mine on the table, not sun-protected. There are lots of reasons why batches can fail, but if you didn’t screw on your lids tightly, that may be why this batch failed for you. Hope that helps.


  35. Newbie question here. We have a family recipe that is similar to yours, but there is no cookinge / peeling of the tomatoes. If I still add salt & lemon juice, does that step matter? Will it affect the fermentation process?

    1. @Megan, I have made this recipe several times, and the last time I made it I didn’t peel the tomatoes (Honestly, just was being lazy). I think it was the best batch I had made so far! So, in my experience, it doesn’t matter about the skin it’s just the salt and whey (or extra salt) that is important for fermenting.

  36. This recipe is delicious but I wonder why I have a white stuff growing over the top. Is it safe to eat the rest. This is my third batch and the first time I have this problem.
    Thanks for the recipe!!!.

  37. I made another batch of fermented salsa, but I am a little concerned because I scooped off a big blob of mold on top, and it still smells a bit moldy. Eat or not eat? I used those jars where the gas escapes, and this is the first time with mold, so a bit perplexed. Also, I am new at this but think it is the cats meow!! SOOOOOOO easy and fast compared to canning! Oh, and I only used salt, no whey.

    1. Same here…I used the perfect pickler lids and no whey and had a glob of white mold on top. I scooped it off and enjoyed the salsa! So amazing!

  38. I was wondering about dried chilis. I have some dried ones here…I thought those might works as most of the recipes I have seen used them…are they important or just for flavor? Also I didn’t see any cumin in the recipe…I am getting into ferments more.

    One of our favorites is Jamacian lemonade. We buy like 40 lbs a month of lemons…so trying lactofermented and pickled lemon rind. We buy organic lemons and remove the zest. Couldn’t bare to toss the white…so pickled it…and it is yummy!!!

  39. Ok, so I made lacto-fermented salsa SEVERAL months ago. When it was first made we tasted it, and it tasted like tomato sauce. (apparently I went wimpy on the spices!) So I popped it in the fridge intending to use it in spaghetti sauce one day… well….. I got it out last night to see if it was bad or what. The jar made a distinct pressure releasing “POP” when I opened it, and then the salsa started fizzing and slowly rising to the top of the jar and overflowing, like a carbonated drink might if you open it too fast. It was so freaky! The stuff smells ok, still not “salsa-y” but certainly not bad. I’m kinda scared to eat it though after that amoeba like performance! Any ideas on what to do with this stuff?

  40. Hi Ann Marie,
    I’m staying off dairy at the moment as part my mission to heal my gut. I can still tolerate foods cooked in home-made organic ghee but have been warned to stay off my own home-made yoghurt which I make with raw milk. That said, does whey count as dairy as far as leaky gut goes? Or do all the milk solids and proteins stay in the strained yoghurt?
    Thanks heaps 🙂

    1. @Jodi

      If yogurt is fermented at home for 24 hours, most people find that they can tolerate it. If you can’t at first, try introducing a little bit at a time and gradually increase.

  41. Pingback: Healthy Salsa Recipe – Fermented Salsa | Food With Kid Appeal
  42. Hi! I just wanted to let you know that we just used your recipe this past weekend to try lacto-fermented salsa (we usually make it regularly…cooking it and all, and still did for 85% of our batch), but yours..YOURS is amazing. Seriously!! I wish we would have trusted the traditionalists and done the whole batch this way…it is simply glorious:o)


  43. do you find that cilantro tastes “weird” after being fermented? After making it last year with cilantro, I thought I might try without and then add when ready to use…

  44. You don’t really need whey if you are using fresh veggies, and if you just salt to taste it will be fine. Just add a little extra salt to account for the fact that juices will be pulled from the veggies thus diluting the brine. I usually salt my ferments until they start to taste a little too salty, then I stop. Lacto-fermentation is pretty flexible and forgiving; precision isn’t normally necessary.

  45. I just tried this recipe and the veggies have separated from the liquid. Is this normal? There’s about 2 inches of yellowish liquid in the bottom of my jars and the veggies are floating right under the lid.

  46. I’ve only ever tried to ferment cabbage and I still haven’t sated it yet. Is the whey necessary? If so what is a good source? We live in a very rural place so I’m hoping it won’t be to difficult.

  47. Is the 1 Tablespoon of salt necessary for the fermentation process or is it more for taste? I made some using 2 T. whey and 1 T. salt and the flavor was wonderful but way too salty. Can I cut back on the salt or will that mess up the fermentation?

    1. I have made this a couple times with only 1 or 1 1/2 tsp salt (to my taste) and 3 T. whey. I didn’t remove the tomato skins (so I probably start with more lactobacilli on the skins since they’re intact and not boiled). Never had any problems with mold. I just finished my last jar that was six weeks old. I wonder if the lime juice also helps create an environment that is friendly to good bacteria and not friendly to mold. (Although I only used 1 T. lime juice per quart.)

  48. Can I use the whey from cream that has been in my refrigerator for 2-3 weeks? Do I have to do anything to it prior to using it in salsa? Can I just strain it and put it in the salsa? This is my first time fermenting. 🙂

  49. You should be aware that most municipal water supplies do not chlorinate the water; they use chloramine, a combination of chlorine and ammonia. Chlorine will dissipate if the water is aerated before using–chloramine will persist. It is harmful to humans, bad for your skin, and it is 100 times less effective killing bacteria (https://www.chloramine.org/chloraminefacts.htm).

  50. when you cover the salsa to leave at room temprature for a few days do you cover it with cloth or put the lid back on the jar?

  51. Hello,
    I have to be honest; I have no idea how I found your website/blog except I was reading about Fermented recipes and found yours for Salsa. Then of course I read another 35 things you wrote and wanted to thank you. You explain things very well; but more important, you have real live ‘links’ to items one might need for your recipes. I looked at almost all the links and found just what was needed, it was so helpful. Thank you again.

  52. Is it ok to leave the seeds in the salsa? I never take them out and I don’t peel my tomatoes either. Will this affect the fermentation process?

  53. Ann Marie-I am really new to fermented foods. This Salsa recipe, if I do not use whey but just add additional sea salt as you state above, will this really become a “fermented food”?

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