You will love this wild fermented salsa without whey. It is packed with nutrients, natural probiotics and live enzymes! The wild fermented salsa is delicious, good for digestion, and free of all major allergens, such as gluten, dairy, eggs and nuts.
You can make the fermented salsa in the fall using tomatoes harvested during peak season, and eat it in the winter. Or you can make it all year round. Try making a probiotic guacamole combining avocado and this fermented salsa, you will be amazed how nature has rewarded us with foods so tasty yet nutritious!
Wild Fermented Salsa is Probiotic and Vegan
I make this probiotic-rich and vegan fermented salsa in September when all the ingredients for salsa are available fresh from my local farmer’s market. It’s the perfect time to ferment and preserve foods for the colder months, as what nature has taught us to do since the beginning of time. I am not a canner, because fermented foods are good for you, and more nutritious than canned.
This fermented salsa is medium spicy. I wanted enough of a kick, but also wanted to ensure my children can eat it too! And most importantly, I fermented this salsa from wild bacteria naturally existing in our environment, without using whey. Hence the word “wild” in the name.
Lacto Fermented Salsa Recipe Without Whey
Whey is a starter culture that’s used in many vegetable ferments, but not at all necessary. The fermentation process will start on it’s own, due to the naturally existing lactic acid bacteria on the vegetables. I choose not to use whey for a few reasons:
- I eat fermented vegetables for probiotic diversity. Therefore, I don’t want my salsa populated with the same strains as my milk kefir.
- whey is not dairy-free. Now people who are dairy sensitive or vegan can still enjoy my salsa and get all the nutritional benefits from it.
- Fermented salsa tends to become watery, especially as it ages. I don’t want to add any more liquid that I don’t have to.
Should I Use Oil Topper in Vegetable Ferments?
Some people use a layer of olive oil on top of the vegetable ferments. This oil layer is added right after the vegetables are filled into the jar on day 0 and before it is fermented, to act as an airlock during fermentation.
I have learnt from the more experienced fermenters that there is a small but real risk of botulism with the oil topper method. You can find a more detailed read on this topic here (you need to be a member of the WFU Facebook group to access the article).
I don’t feel the gain is worth of the risk, therefore I don’t use oil topper in my vegetable ferments. For extra flavour, I can always add the olive oil at the time of eating.
Should I Use Citrus in Fermented Salsa?
Most salsa recipes, fermented or not, call for lemon and lime juice. I am not so strongly objecting citrus in the salsa as I am for oil topper and whey. However, I choose to omit lime and lemon too in this recipe, for the following reasons:
- I don’t want to add more liquid that I don’t have to, as there is already quite an amount of juice in the salsa.
- Once the salsa is fermented, it will be very sour. Therefore, you won’t really miss the note of the lemon and lime.
- If I don’t add citrus, the salsa mixture is less acidic to begin with. Therefore, I can let it ferment a little longer to maximize the benefits from all the good bacteria that had a chance to develop.
If you really love the flavour of citrus, go for it. If you do choose to add lime or lemon, 1-2 is enough for this recipe. I personally prefer lime in salsa over lemon, as the flavour profile of lime works better in the salsa.
How Long Does Fermented Salsa Last?
As long as you ferment the salsa properly, you can store the fermented salsa in the fridge or cellar for months to a year. Every year, I make a big batch in the fall. And I have personally eaten my fermented salsa throughout a whole year. However, tomato salsa is the kind of ferments that aren’t meant for or required to age, unlike the sauerkraut.
The flavour of the salsa are great throughout the year of storage, but the tomato chunks do become mushier and the salsa becomes more watery as time goes by. This is because the bacteria will slowly digest the tomatoes. If you like a firmer texture, then you will want to eat this salsa in the first few weeks once fermented.
Serving Suggestions
My favourite way to pair this fermented salsa is to add a few scoops to some chopped avocado. It makes a quick and tasty probiotic guacamole! Another way to enjoy the salsa is to use as a topping on your scrambled eggs and pan-seared fish. You can always use fermented salsa rather than regular salsa in any Mexican dishes for extra nutrients. Furthermore, you can use this salsa on pretty much anything instead of fresh tomatoes too, such as burgers, salads and sandwiches. There are many great ways to incorporate a little probiotic food everyday.
Related: More Gut-Healing Fermentation Recipes You Will Love
- Fermented Pickles /w Green Tea and Dill Flowers
- Pineapple-Turmeric-Ginger Probiotic Sauerkraut
- Homemade Fermented Sauerkraut /w Caraway Seeds
- Paleo Apple-Fermented Kimchi
- Keto Kimchi (Whole 30, GAPS, Paleo)
- Honey Fermented Garlic: A Natural Remedy for Cold and Flu
- 11 Important Things to Know for a Successful Kombucha Brew
- Kombucha Carbonation and Flavouring Tips: The Second Fermentation
- Probiotic Kefir Tzatziki Dip
- Raspberry Kefir Cream Cheese Spread
- Injera (Fermented Ethiopian Teff Flatbread)
- Overnight Banana Spelt Pancakes: Fermented for Better Nutrition and Digestion
- Kefir Fermented Honey Thyme Sourdough Cornbread

Wild Fermented Salsa
Ingredients
- 6 lb tomatoes (select a firm and less juicy variety; I use "San Marzano")
- 1 lb red onion (approx. 2 to 3 onions per pound)
- 1 lb sweet red peppers (approx. 2 to 3 red peppers per pound)
- 4 jalapenos
- 12 garlic cloves
- 2 cup chopped cilantro
- 4 tbsp sea salt
- 1 tsp ground cumin
Instructions
- Remove and discard ends of the tomatoes where stems are attached. Save the juice and seeds of the tomatoes in a small bowl. This way you won’t waste all the juice and make a big mess when dicing the tomatoes. Dice the tomatoes and store in a large bowl.
- Dice 1-2 onions, and add them to the large bowl with the tomatoes. Save rest of the onions for blending later. I like to see chunks of onion in the salsa, and also like the flavour of the onion blended in the sauce, therefore I divide them to dice half and blend the other half. For simplicity, you can choose to dice all the onions or skip this step.
- Remove and discard seeds and stems of the sweet peppers and jalapenos. Put sweet peppers, jalapenos, garlic cloves, rest of the onions in the food processor. Add the saved tomato juice from step 1 to the food processor. I use all the juice of the “San Marzano”, but other tomato variety may produce too much juice. In that case, you can leave some juice out, else your salsa will be too runny. Pulse the food processor until all the ingredients are evenly mixed, but not to turn it into a smooth blend. It should resemble a thick sauce with small chunky bits insides.
- Add the mixture from the food processor, chopped cilantro, sea salt, ground cumin into the large bowl where the diced tomatoes and onions are stored. Combine all ingredients well.
- Fill the salsa in glass jars. Make sure to push down the salsa to release all trapped air and have the vegetable chunks submerged under the juice. You want to fill the jars close to the top, leaving roughly an inch of air space to the rim. Seal the jars loosely so that air can escape, otherwise you will need to open the jar every day or 2 to release the pressure.
- Let it sit in a dark spot away from heat for 3-5 days. If your house is cold or if you like your salsa more tangy, then you should ferment the salsa on the longer side of this range. Otherwise, you can ferment it for a shorter amount of time. It’s normal to see air bubbles produced in the salsa around day 3 – this is a sign of fermentation and will continue for a few days – you may need to push down the salsa gently with a fork to help release the air. You can taste it daily until it reaches the acidity you desire, and then move the salsa jars to cold storage to slow down fermentation.
Nutrition

A friend gave me a jar of this salsa last month and I’m hooked! So I made a small batch 3 days ago. Today when I checked the jars they all have a whitish skim on the top. What is this… and what should I do about it? Is it spoiled? Thanks so much!
I live in Nepal, so I have to soak my vegetables in a chlorine rinse (or iodine) to ensure safety when eating raw vegetables. I don’t love the taste of raw tomatoes so I’ve never enjoyed fresh salsa. But I’m told that the fermenting process changes the taste enough that I may just like it, so I’m giving this a go. I’m concerned though that my need to kill all the potential bad bugs has also killed off all the good ones… is this a situation where you would recommend using a starter like whey, just in case? Or do you think leaving the cleaned veggies out on my counter uncovered for a few days would be enough to repopulate the natural bacteria and yeasts?
Hi Erin! I think in your situation, it’s probably a good idea to add whey as a starter. I have heard stories from people who ferment in some countries due to local water / environmental reasons the fermentation turned out to be unsuccessful. So yes, the lack of good bacteria or the condition to allow them propagate is a concern.
Thanks for the feedback! I put it all together last night so we’ll see how it goes! I did add a small amount of kefir whey. Loving the smell of it already!
Hello ! I found this on the internet. I made these about 3 days ago and stored how you said but I feel like the top of mine have gone mouldy. What have I done wrong ? I spent so long cutting everything up. They are in a dark pantry with the lids loose as suggested but going mouldy instead of fermenting. Help ! Maybe I did not add enough salt. I am so disappointed.
Hello,
Do I close the lids when I put the Jars to a cooler place? I mean after fermentation has started and when I want it to slow down.
Thanks for sharing! I made this, but the mixture tastes very salty. It hasn’t started fermenting yet. Is that normal? I’m expecting flavours to change somewhat over the next few days.
This recipe makes about 3.5 to 4 quarts of salsa, and there is only 4 tbsp of salt in it, which is not high at all compared to other fermentation recipes out there. One thing about the weight of the vegetables in the ingredient list, is that they are excluding the cores and trim-off, so they all into the recipe. If you take a pound of pepper, and then remove the tops of cores, you will end up much less.
Hello I’m Curious if this will still work if i fire roast a few of the tomatoes to give it the traditional roasted salsa flavor. But keep everything else raw as to keep the microbes healthy? Bless Up
HI Juan, I have not done that, so I don’t know for sure. I think as long as you keep the fire roasted tomato to a less percentage, it may still work and the only way to find out is by trying. Although I stated the reasons why I don’t use whey or another starter culture in the vegetable ferment recipes, here is a scenario where you can consider introducing extra culture, while still achieving the flavours of a cooked tomatoes. Hope this helps. 🙂
The picture at the top of the post looks like the jar is filled to the brim. Is it necessary to leave any head space when putting the salsa into jars to ferment?
Thanks!
Hi Debbie, I do have to keep my food photography in style, thus you see the jar is filled all the way to the top. Yes, it’s necessary to leave head space when putting the salsa into the jars to ferment, unless you don’t mind expansion and possibly salsa juice spilling out. Also make sure the solids are submerged under the liquid. These photos are presentations of the salsa after fermentation has completed.
I made your recipe but for some reason it seems too salty. Can I use less salt and still be safe?
Hi, Anita! That’s very interesting to hear. My fermented salsa hasn’t turned out salty. If you do the math based on the ingredient section then you can see, I use roughly 1 tbsp of salt to 2 lb of vegetables. Typically people ferment with a ratio of 3 tbsp of salt to 5 lb of vegetables. But taste is individual, and if you still find it salty, I think you can reduce the salt. The key is to monitor your ferments. If it doesn’t grow mould and doesn’t taste/smell bad, then it’s good.
Have you tried adding mango?
I haven’t tried adding mongo to this recipe, but I would encourage you to try. Sounds like they would be yummy to ferment together! ❤️
This seems like the perfect salsa recipe! I don’t know much about fermentation, so I really enjoyed all the extra information you infused into this post. Beautiful work!
Thank you so much Justine! I am glad you found the information helpful. Hope you get to try this recipe some day 🙂
LOVE this recipe! I’ve made salsa many times but usually eat it right away or can it for the winter, but I’ve never been patient enough to ferment it. hahaha I completely agree with you about the other methods, I also prefer to ferment things naturally in order to benefit from the variety of natural bacteria. Well done! I might give this a try when tomatoes are in full harvest
Thank you for the kind words, Gabrielle! I think you will love this one 🙂 Fermented salsa is one of the best to start with for the impatient fermenters, as it requires shorter fermentation time than many other ferments. The tomatoes are starting to show up in bushels in the markets, and I will surely be making some more this year!
storing this for year 🙂 great idea!!!
It sounds scary at first. But the properly fermented vegetables really last for a long time. I never tested how long, as I finish them by 1 year. Usually I have to ration my ferments if I don’t want to make another batch before the peak season arrives 🙂
I love fermented flavours and salsa. Putting this on my to make list.
Thank you. I hope you like it as much as I do!
Thank you so much for your thoughts and analysis section at the end. It really helped me finalize what recipe I’ll be using and also helped me tweak another fermenting recipe I’ve been working on.
Michelle! Thank you so much for your kind words! I am really glad you found the last section helpful. I can’t help with my analytical nature to wonder and explore all the options – probably that’s why many of us love fermenting – half creativity and half science, right!?!. I would love to hear from you how your salsa and other fermenting recipe turn out! 🙂
I’m so excited that you have a blog, Yang! And I’m going to have to try this first recipe. Looks so good!! <3
Thanks Kristy! Let me know how it goes 🙂
Fabulous, Yang! I can’t wait to try this out. It will be nice to skip the process of canning which calls for immersing bottles in a hot water bath. Cheers!
For sure, Gwen. Fermenting really is much simpler once you get a hang of it! Knowing all the nutrition you are feeding your body is another win. Just be sure to pick a good variety of tomato – it makes a big difference. I can’t wait to hear your result!