If you follow me over on Instagram, you know all about my obsession with making and eating homemade salsa. But this isn’t just any homemade salsa; it’s fermented salsa.

Salsa meets gut-loving probiotics and the most amazing flavor!

Fermented Salsa: The Best Homemade Salsa Ever

A few months ago, Sarah from St. Pete Ferments joined me on the podcast to talk about ferments. In the podcast episode, Sarah shares why consuming fermented food is important, particularly ferments that are made in your local area. You can listen to the episode below.

Since talking with Sarah, I have a renewed interest in making homemade ferments in my own kitchen. I’ve made sourdough on and off over the years (mainly off now because I have a wonderful local source) and just recently started making my own sauerkraut.

Since having Sarah on the podcast, I’ve also started following Hilary Boynton, Live Yum Yum on Instagram. Hilary is reforming the way schools cook and serve lunch. And she’s on a mission to get back to real, traditional food. A month or so ago, Hilary made fermented salsa on her Instagram Stories. She made it look so easy. Naturally, I had to try making this fermented version of salsa.

chopped tomatoes for salsa

And that I did.

I documented the initial process on Instagram. And then again on Instagram because the first attempt was such a success. And then again. Each time, friends on Instagram sent me messages requesting the recipe.

tomatoes for salsa

What is Fermented Salsa?

Fermented salsa is simply salsa (tomatoes, cilantro, garlic, pepper, onion, and salt) that’s been left at room temperature to allow the good bacteria to populate the salsa.

In more technical terms, fermentation is the breakdown of sugars, by the enzymes of microorganisms, that turn into natural yeast and bacterial growth when oxygen isn’t present. Veggies are naturally covered in lactic-acid bacteria, so when the veggies are submerged in a salted brine, the good bacteria naturally begins to ferment the food. This is the case with tomatoes and other veggies used to make fermented salsa.

chopping cilantro

Now, I know you’re probably thinking, “Wait, but won’t the bad bacteria take over and produce awful, rotten salsa?” Let’s talk about that…

Salt is added to the initial fermentation of the salsa to prevent the bad bacteria from growing before the good guys get to work on populating the salsa mixture. So there’s no need to worry. Fermentation is a very natural and beautiful process. I know it sounds scary, but it’s not.

Why Ferment Salsa?

So why not just make salsa? Why take the time to ferment the salsa? There are a few reasons…

adding garlic to the salsa mixture

1. Fermented salsa tastes amazing. 

Fermentation adds a deliciously tangy flavor to foods. That’s all thanks to the bacteria and natural yeasts at work. Fermentation takes cabbage, in the case of sauerkraut, and turns it into a slightly sweet and tangy food. It takes tea and sugar, in the case of kombucha, and makes a bubbly, slightly sour (in the very best way) tea. In the case of salsa, fermentation lends a slightly tangy flavor that’s hard to resist.

adding lime juice to salsa mixture

2. There’s also the probiotic benefit.

When you ferment fresh salsa, you end up with a bacteria-rich food. And do you know what thrives on good bacteria? Your gut (and immune system).

Having a gut that’s healthy and thriving is incredibly important. This is why people take probiotic pills today. And while I certainly think supplements have their time and place, I believe food should always be our #1 source when possible. Instead of instantly turning to a pill, we need to get back to consuming fermented foods, just like our ancestors did for thousands of years. An easy, natural, and budget-friendly way to populate your gut with good bacteria is to simply consume more fermented foods in your daily diet. This could include fermented cheese (real cheese, not a cheese product), yogurt, sauerkraut, salsa, kimchi, and kefir.

adding salt to the salsa mixture

3. Fermentation preserves the salsa. 

For thousands of years, people have fermented foods. Before refrigeration, fermentation played a major role in preserving a bountiful harvest (from the garden) or a large amount of milk (which would be turned into cheese). Fermentation encourages the growth of good bacteria so the bad bacteria doesn’t take over (causing food to spoil and rot). If you make regular salsa, it will likely go bad within a few days. When you ferment salsa, you extend the life of the salsa for up to a couple of months.

adding salsa to a jar to ferment

How to Ferment Salsa

Making fermented salsa is a super easy process. If you can chop some tomatoes and onions, and mince some garlic, you can ferment salsa. You don’t need any special fermentation tools, a culture or whey, or prior fermentation experience.

To begin, cut the tomatoes into small pieces, chop the onion and spicy pepper, mince the garlic, and chop the cilantro. Then add these ingredients to a large bowl, along with lime juice and salt. Mix the ingredients together and then add everything to an air-tight, glass storage container.

adding salsa to the jar to ferment

Now, here’s the key. Once you get all the salsa in the jar, add the juice/brine found at the bottom of the bowl to the jar, and then push the salsa down with your hand (fist) to ensure the veggies are fully covered in the juice/brine. This takes some faith at first, because it doesn’t seem like there’s very much juice/brine compared to veggies. But, trust me, there’s enough juice/brine to cover the veggies.

Once the veggies are fully submerged in the brine, add a weight on top. You can use half of a bell pepper, a clean rock, a cabbage leaf–anything that will keep the veggies underneath the juice/brine.

adding a weight before fermentation

Your Family Will Love Fermented Salsa

Okay, that’s a bold statement to make. I can’t guarantee that your family will love fermented salsa, but I can say from experience that my family remains very apprehensive about fermented veggies but loves fermented salsa.

Cheese? They’re down with.

Yogurt? Yes!

But sauerkraut, kimchi, or the fermented carrots that I purchase at market? Nope, they’re skeptics.

fermenting salsa

Salsa, on the other hand, has been the key to introducing fermented veggies into their diet. Even Dustin, the greatest fermented foods skeptic of all, loves this salsa and asks for second and third helpings.

Getting the salsa ready for fermentation

What Else Can You Ferment?

Once you make fermented salsa, and realize just how easy it is to make your own probiotic-rich, fermented foods, you may want to branch out and try making other ferments. I’m still in the branching out phase. I’m slowly learning how to do more, and with each success my fermentation confidence grows. Here are a few ideas for what else you can ferment…

serving fermented salsa with chips

  • Fermented Carrots: Next on my list to make. I love the fermented carrots found at the market (from St. Pete Ferments), now it’s time to make my own.
  • Fermented Salsa Verde: Branch out from red salsa with this green salsa made with tomatillos.
  • Ginger Bug: This is another ferment on my list to try.
  • Kefir: One of the easiest ferments you can make. Use kefir to make smoothies (as all or just some of the liquid), yogurt sticks, or Ranch.
  • Sauerkraut: A classic and so easy to make.
  • Fermented Vegetables Cookbook: An incredible cookbook/guide for making fermented veggies at home.
Fermented Salsa: The Best Homemade Salsa Ever
4.42 from 31 votes

Fermented Salsa

The best homemade salsa you'll ever make and eat, and it's full of probiotic goodness. Super easy! No prior fermentation skills or special equipment needed.
Kristin Marr
Prep Time30 minutes
Cook Time0 minutes
Initial Fermentation Resting Time2 days
Course Condiment, Side Dish, Snack
Cuisine American, Mexican
Servings 6 cups
Calories 47 kcal


  • 2 lbs cherry or grape tomatoes chopped
  • 6 garlic cloves minced, or to taste
  • 1 jalapeño pepper chopped, or a serrano pepper
  • 2 cilantro bunches chopped, just the leaves not the stems, depending on taste preference. I like a lot of cilantro. You could also skip the cilantro if desired.
  • 1 medium red onion chopped (about 1-2 cups once chopped, depending on taste preference)
  • 2 limes juiced
  • 1 TB salt I use a fine salt (meaning the grind is fine, not coarse). Use a mineral-rich salt, like Redmond's Real Salt.

Special Equipment:

  • large bowl
  • 2 liter glass jar with an air-tight lid
  • weight such as: half a bell pepper, cabbage leaf, half an onion, a clean stone, or fermentation weight


  • To a large bowl, add the chopped tomatoes, minced garlic cloves, jalapeño pepper, cilantro, red onion, lime juice, and salt. Toss to thoroughly combine.
  • Taste the salsa. It should be salty, but not overpowering. If you can't taste the salt at all, add a few more pinches. You don't want a super salty salsa, but you should taste the salt. The salt is key in aiding the fermentation process and keeping the "bad bacteria" from populating. I usually add a bit more salt, after the initial 1 tablespoon. Use your sense of taste as your guide.
  • Add the salsa to an air-tight glass jar. I use a 2 liter jar from Fido (pictured in this post). Ball Jars also work well. You may also divide the mixture between two jars, if needed.
  • Once all the salsa is added to the jar, add the brine/juice left at the bottom of the bowl to the jar.
  • Press the salsa down in the jar so the veggies are fully submerged in the juice/brine. Then add your weight of choice. I've been using half a bell pepper as a weight. This is used to keep the veggies fully submerged in the juice/brine. The weight, if perishable, will be tossed at the end of the fermentation process (unless you're using a stone).
  • Tightly seal the jar and place in a spot that's away from direct sunlight. Ferment the salsa at room temperature for 2 day (48 hours). You should notice, after about 24 hours, that bubbles begin to form in the salsa. This is part of the fermentation process as it comes "alive." The bubbles won't be super fizzy or aggressive, but should be apparent.
  • After 2 days, your salsa is ready to enjoy. At this point, you can immeadiately open the jar and eat the salsa or store the salsa in the fridge (it will keep for a couple of months). Either way, open the jar and remove the weight. If you choose to store the salsa in the fridge, the fermentation process slows down, but the flavor will continue to develop so keep this in mind.
  • Use this salsa just like any fresh salsa: topped on quesadillas or enchiladas, in tacos, with chips (Jacksons Honest's or Siete are our favorite brands), etc.


I've purposely adapted this recipe to make a large amount because...
1. we go through this salsa quickly 
2. it does take some time to chop the veggies and I want to use my time wisely (making enough to last multiple snacks and meals) 
3. it keeps in the fridge for a couple of months, so there's no need to use it up super fast 


Calories: 47kcalCarbohydrates: 11gProtein: 2gFat: 1gSaturated Fat: 1gSodium: 1181mgPotassium: 391mgFiber: 2gSugar: 5gVitamin A: 820IUVitamin C: 46.2mgCalcium: 34mgIron: 1.3mg
Tried this recipe?Let me know how it was!

Fermented Salsa: The Best Homemade Salsa Ever


  1. Hi there! My family is absolutely obsessed with this recipe? Have you tried canning it? I’d like to make larger batches but don’t have the refrigerator space

    1. Hey Monika, So glad you love the salsa. The beauty of fermentation is that it preserves the food without the need for canning. Since fermentation deals with raw food, the processing from canning will cause the food to lose the benefits of such food. The salsa will keep in the fridge for many months–as fermentation naturally preserves the food. So you could make a large batch and store in the fridge.

  2. I want to try this, but am concerned that one jalapeno for 2 lbs of tomatoes might not be spicy enough. We generally like things with a medium amount of heat. I know that the hot peppers I grow vary widely in heat level though, so I don’t want to add too many! Do you think 3 would be too hot? Does the fermentation decrease the heat level like pickling does? Thanks

  3. Good morning! This recipe looks great. I’m wondering…In the past, I’ve made fermented salsa with a bit of leftover whey from my homemade yogurt. Could I add this to help in the fermentation process? Would I lessen the salt perhaps?

  4. HELP please – I followed directions and now at 48 hours there isn’t a bubble to be seen. I have fremented before and know the bubbles should be apparent by now. I can’t understand why they aren’t. Should I add more salt, throw it out, or eat it?

    1. Hey Mara, The bubbles will not be super active or bubbly, but they should be apparent throughout the salsa. Do you see any air pockets (bubbles) in the salsa mixture? If so, you’re good. You can taste the salsa and if you like it, then you can stick it in the fridge and enjoy. If you want to go another day or two, you can do that. The salsa will continue to ferment in the fridge, it just slows the process down. Adding more salt will SLOW the fermentation process down. I made an Instagram Live video showing the entire process and what to look for. You may find it helpful: https://www.instagram.com/tv/CAlZedNpOHO/?utm_source=ig_web_copy_link

      1. Hi Kristin,
        I cleaned out the last of my COVID garden, frost tonight. I am playing with fermenting and this is my second venture. I liked your recipe and it is similar to what I normal use to can Salsa. I did not have limes, but my old recipe used cider vinegar. Without thinking, I dumped some in with the other ingredients. Have I ruined it with the vinegar? Almost 5# of vegetables and 1/2 cup cider vinegar.
        I hope you can let me know. If I have ruined it, maybe I can salvage all those veggies. Thanks so much!

  5. I have some whole frozen tomatoes in my freezer from last year’s harvest & was wondering if they can be thawed & used to ferment a “runny” salsa?

    1. Hey Melinda, That’s a good question. I’m not sure. If they haven’t been cooked, that may work. If they have been cooked, they I don’t think they’ll work for this. I would google using frozen produce for ferments and see what comes up.

  6. 5 stars
    Love this salsa! My husband was skeptical initially but he loves it! We make it all the time now.

  7. I have some pico de gallo that I made with these same veggies, however I also added some dried spices. I put it together 4 days ago… do you think I could take it out of the fridge and try to ferment it at this point? Or should I start fresh?

      1. I started chopping veggies for salsa a few days ago, but got interrupted by other jobs/kids; I put my bowl of veggies, dried chilies and canning salt in the fridge with the intent of getting back to it later in the day… now a few days later in my search to see if it’s still possible to use or if I need to throw it out, I came across your recipe… since I put salt in it, can I add lime and do fermentation, or do I also need to start fresh? Thanks!

  8. Have you ever put these in a blender to make it more saucy yet chunky? In Texas we would call your recipe more like pico de gallo vs a runny mixture called salsa.

    1. Hey Brenda, Yes, you can do that. It can speed up the fermentation process, so just keep an eye on the salsa. Blend all the ingredients in the blender and then add the salt and ferment.

      1. I like a more runny salsa as well versus pico. When you say that it could speed up the fermentation and to keep an eye on it, what exactly would I be looking for? I have never fermented anything so I am not exactly sure what to look for.

      2. Hey Penny, You’ll notice air pockets begin to form in the salsa. I just made a batch last night, and blended it up versus making a thick salsa (pico). Today, the air pockets are very noticeable versus the thick (pico) salsa usually take a bit longer for the air pockets to begin to form. The air pockets are a sign fermentation is taking place. So, I may only ferment this salsa for 24-36 hours versus the full 48 hours. There’s nothing wrong with going longer, but it may be more tangy. It’s perfectly safe to go the full 48 hours or longer. Also, when you blend, just make sure everything is submerged in the liquid, and separation may occur in the jar. That’s normal and perfectly fine.

  9. So excited to make this today and love all of your recipes! Do you keep all the seeds from the jalapeno? Does the 1 jalapeno make it mildly spicy?

    1. Hey Laura, Thank you. I recommend removing the seeds, particularly if you don’t want a spicy salsa. It will depend on the jalapeno. Some jalapenos have no heat while others do. Enjoy!!

  10. I am using tomatoes from my garden and am not sure what 2 lbs looks like. Do you know how many cups approximately that would be? Thanks!

  11. Hi there! This smells and tastes amazing. One question, when I made it there was not quite enough liquid so I added a little water, just enough to submerge. Could that affect the balance in the fermentation? I didn’t see many bubbles and wondered if that was why. Taste was still great and now I’ve put it in the fridge. Thanks for all you do!

    1. Hey Tami, The bubbles are more air pockets forming in the salsa than actual bubbling action. There shouldn’t be an aggressive bubbly with this ferment. Once you’ve really squished down the salsa in the jar, if there isn’t any liquid to submerge the salsa, you can add water, that’s fine, or add more lime juice.

  12. 4 stars
    Update: sent the salsa with my husband’s lunch and got a text saying salsa is delicious, we should never buy salsa again!

    The reason I only gave 4 stars is that I made 1/2 recipe and used a whole jalapeno pepper, but there was no heat at all. Maybe I need to add more, or maybe I just got a dud. Either way, the salsa itself is delicious!

    1. That’s amazing, Sarah!!! Yay, so happy to hear that. Yea, jalapenos can vary greatly in heat. Many just aren’t hot these days. Next time, go with a serrano. Or, add a couple of serrano peppers.

    2. This is way past when you posted, but just for others’ general info, I’m pretty sure I’ve read that jalapeños lose some of their bite when they’re fermented. Maybe a little fresh jalapeño (not fermented) added at serving time wouldn’t hurt,

  13. Made this tonight so I can’t comment on final outcome yet, but just wanted to share a tip. We prefer our salsa a little less chunky, so I used a food processor to chop the veggies finely. Worked great, and way faster then fine chopping by hand! I did each veggie separately, scraping the chopped veggies into a bowl in between, being careful to get all the liquid.

  14. Thank you Kristin for this recipe! For our family I will add less onion next time or maybe instead of using a red onion like I did maybe I will use a sweet onion. I used a large jalapeno and when I tasted the salsa fresh, before fermenting, I thought I had gotten it too hot for my grand-kids, but after fermentation it was not as hot. I also thought I might add a bit less cilantro to the batch and then add some fresh when served. Even though I have made fermented foods before, I was skeptical that fermented salsa would last that long, but it is still delicious and like you said, the flavors continue to develop. This is a recipe that will be used over and over for our family. Thank you!

  15. I get an abundance of heirloom tomatoes in my CSA box, this would be perfect to use them up. How do you think they would do compared to cherry/grape tomatoes?

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