The Best Fermented Tomato Salsa You’ll Ever Make
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When the tomatoes are comin’ in hot in the summer, I have a half gallon jar of this fermented tomato salsa recipe going’ at all times. Â Maybe a quart if I’m not trying to be obnoxious. Â BUT oh my goodness, fermented salsa speaks to my soul. Â The flavor. Â The tangy taste. Â The beneficial bacteria. Â It is EVERYTHING and one thing I look forward to every summer. Â
I will only use tomatoes I have grown, or from other farms that have the same values as me, to make fermented tomato salsa… or well, really can anything tomato. Â I don’t want the store bought tomatoes that are covered in weird waxes and other mystery things. Â Plus… they just don’t have the flavor I want. Â Home grown is the BEST and I’ll hear no more about it.

Once you start fermenting fruit, and even vegetables, it becomes second nature. Â It is crazy easy and a wonderful way to quickly preserve fresh produce. Â Once I got a batch or two under my belt I was like okayyyy I can do this. Â And if you start with this fermented salsa… you will never be the same. Â You’ll be off fermenting everything but your big toe in no time! Â
The fermentation process is basically a controlled rot of your food… we let it rot, but control which bacteria take over. Â We add salt and the existing acidity of the food to encourage the good bacteria to take over for lacto fermentation. Â Those bacteria slow down the rotting process and make it less likely for some enzymes and bad bacteria to want to mold or destroy the food. Â Instead, what we’re left with is a salsa that our gut LOVES. Â I have found, specifically for me, consuming a diet heavy in traditionally fermented foods makes me feel amazing and is great for my immune system. Â I know that’s not the case for everyone though.
Tips for Successful Fermented Tomato Salsa:
- When using a culture from a previous ferment, make sure the ferment was good to begin with and not contaminated or gone bad. You can tell a lot from sight, smell, and taste.
- Use mason jars/glass jars for fermentation so you don’t have microplastics in your food. They’re easy to sanitize and reusable.
- Sanitize fermentation vessels along with any weights and tools you will be using. Â This prevents cross contamination.
- Don’t put your ferments in direct sunlight. Â Sunlight kills the cooties, both the good and the bad. Â We NEED that bacteria to successfully preserve our fermented tomato salsa! If the wrong bacteria takes over, you’ll have a stinky mess on your hands.
- Store ferments at room temperature during the initial fermentation phase.
- Cold storage when the ferment is to your liking is best to slow/stop fermentation.
If you’re looking for a good homemade salsa recipe for canning instead of this fermented tomato salsa, check mine out:

​What is Sweet Whey?
In my recipe, I call for the juice of 1 lime. Â You can substitute about 1-2 tablespoons of bottled lime juice or use sweet whey. Â What on earth is that?! Â Sweet whey is the byproduct of cheesemaking in cheese recipes where rennet is used to coagulate the milk instead of an acid. Â
I normally use the whey from my homemade chevre or yogurt. Â It adds a tang, and some extra probiotic goodness and oooopmh to my ferment, with something that is a byproduct of something else I made :D Â You don’t need it though and lime juice is just as delicious, but I live in Ohio. Â We don’t have citrus trees and I don’t like to go to the grocery store. Â So, sometimes my lime juice is just separated cheese juice. Â Kay?! Â If you do choose to add whey, you can choose not to add liquid from another ferment as whey does the job. Â
Let’s make some homemade fermented tomato salsa with fresh tomatoes!
Equipment You Might Want:
- Wide Mouth Quart Jars
- Glass Fermenting Weight
- Fermentation Lid
Salsa Ingredients:
- 2 cups diced tomatoes, cored & diced
- 1 bell pepper, diced
- 1 jalapeno, diced
- 1 onion, diced
- 2 cloves garlic, minced
- 2.5 tsps salt
- 1 lime (1 Tbs bottled lime juice or sweet whey)
- Fresh cilantro, optional
Step 1: Prep
Cut all the ingredients into sizes you enjoy. If you prefer a chunkier salsa, do that. I prefer small pieces, so I chop most everything pretty small. You do want to leave it as a somewhat chunky salsa so it ferments correctly as opposed to making a blended, smoother salsa in your food processor. That will not work well.
In a large bowl, add all ingredients. Stir to mix well and let sit for a few minutes to get the juices flowing.
Step 2: Fermenting
Once you notice juice in the bowl, add contents to a wide mouth quart (32 ounce) size jar.
Gently mash with the clean handle of a wooden spoon until juice covers everything.
Push down and cover with a glass fermentation weight. Anything that will hold all the veggies under the salty liquid to keep them from molding.
Add a fermenting airlock lid and set aside out of direct sunlight for 2 days to ferment at room temperature. On day 2, taste to see if the salsa is tart enough. If not, let it ferment until you enjoy it. I will, on occasion, let mine go 5-7 days. Fermentation time varies between kitchens, so I can’t give you an exact time.
You will notice small bubbles form and that’s a good sign that fermentation is taking place! Those bacteria create gas bubbles.
Step 3: Storing
Once fermented to your liking, place in the fridge and consume within about 3 months!
Eat this fresh salsa cold to preserve the nutritional benefit of the ferment. We use it with tortilla chips for a delicious snack or to pile on top of tacos made with homemade fresh milled tortillas. So good!
Notes:
Familiarize yourself with what kahm yeast looks like on ferments compared to mold. If your ferment is bad, you will know by the smell and appearance. It will take on a murky, cloudy look and not smell appetizing. A good ferment will smell tangy and pleasant, not like someone’s rotten foot fell off and died in your jar.
Enjoy this delicious way to quickly preserve those garden fresh tomatoes you either grew or snagged at the farmers market!

Equipment
- Wide mouth quart jars
Ingredients
- 2 cups diced tomatoes cored & diced
- 1 bell pepper diced
- 1 jalapeno diced
- 1 onion diced
- 2 cloves garlic minced
- 2.5 tsps salt
- 1 lime 1 Tbs bottled lime juice or sweet whey
- Fresh cilantro optional
Instructions
- Cut all the ingredients into sizes you enjoy. If you prefer a chunkier salsa, do that. I prefer small pieces, so I chop most everything pretty small. You do want to leave it as a somewhat chunky salsa so it ferments correctly as opposed to making a blended, smoother salsa in your food processor. That will not work well.
- In a large bowl, add all ingredients. Stir to mix well and let sit for a few minutes to get the juices flowing.
- Once you notice juice in the bowl, add contents to a wide mouth quart (32 ounce) size jar.
- Gently mash with the clean handle of a wooden spoon until juice covers everything.
- Push down and cover with a glass fermentation weight. Anything that will hold all the veggies under the salty liquid to keep them from molding.
- Add a fermenting airlock lid and set aside out of direct sunlight for 2 days to ferment at room temperature. On day 2, taste to see if the salsa is tart enough. If not, let it ferment until you enjoy it. I will, on occasion, let mine go 5-7 days. Fermentation time varies between kitchens, so I can’t give you an exact time.
- You will notice small bubbles form and that’s a good sign that fermentation is taking place! Those bacteria create gas bubbles.
Storing
- Once fermented to your liking, place in the fridge and consume within about 3 months!
- Eat this fresh salsa cold to preserve the nutritional benefit of the ferment. We use it with tortilla chips for a delicious snack or to pile on top of tacos made with homemade fresh milled tortillas. So good!

















This is by far our favorite salsa now! Thank you for sharing the recipe with us.