This chunky Low FODMAP Instant Pot Salsa adds some zesty, IBS-friendly deliciousness to tacos, burritos, chips and more! Calling for either canned or fresh tomatoes, this low FODMAP salsa recipe is made flavorful in the Instant Pot and last longer in the refrigerator than homemade fresh salsa. In addition to being low FODMAP, this salsa is also Keto, low carb, Paleo, Whole30, and vegan when eaten with compliant chips!
Please note: this recipe, although low FODMAP, contains spicy ingredients, which may still trigger symptoms in some (but not all) people with IBS. See "Spicy Food Warning" section below for further information.
Jump to:
- Is store-bought salsa low FODMAP?
- Why Low FODMAP Salsa in the Instant Pot?
- Is this low FODMAP salsa suitable for canning?
- Low FODMAP, Low Carb, Keto, Paleo, and Whole30
- Spicy Food Warning
- Necessary Equipment
- Low FODMAP Instant Pot Salsa: Ingredients & Success Tips
- What can I eat this low FODMAP salsa with?
- Chunky Low FODMAP Instant Pot Salsa
- Related Recipes
Is store-bought salsa low FODMAP?
Most store-bought salsas contain some sort of high FODMAP ingredient, typically garlic and/or onion. However, the brand Fody makes mild and medium low FODMAP salsa that can be found at some stores in North America. They can sometimes be found in the "Natural Foods" aisles, at health food stores, or purchased on Amazon. However, it is more cost effective for me to just make my own low FODMAP salsa in the Instant Pot. In doing so, I also can control the flavors and chunkiness level to my own personal taste.
Why Low FODMAP Salsa in the Instant Pot?
There are a lot of low FODMAP salsa recipes out there, but many of them are fresh salsa recipes. I am a fan of certain fresh salsas like my homemade Low FODMAP Pineapple Salsa Fresca, but unless it's eaten fairly quickly, fresh salsa of any kind doesn't keep for very long.
Stewed salsa, on the other hand, when prepared with the right ingredients, can last much longer and sometimes even be canned. Using the Instant Pot to make salsa brings such amazing depth of flavor in a short amount of time. Plus, I hate to have things boiling on the stove during the summertime, warming up my house. Containing the boiling within the Instant Pot is my summertime preference.
Also, because we are stewing the salsa and making it garlic-free, we can easily incorporate some amazing garlicy flavor without the FODMAPs by using garlic-infused olive oil. We sauté some of the veggies with garlic oil and they absorb much of the oil, leaving very little oil residue throughout the salsa.

Is this low FODMAP salsa suitable for canning?
This particular low FODMAP salsa recipe could probably be canned. However, I am not an expert in canning, so my instructions only cover how to make a salsa that can last in the refrigerator in an air-tight container for up to two weeks. I created this recipe with the possibility of canning in mind but will allow the canning experts to decide if and how to can it.
This recipe also makes a small batch - only about 5 cups total, which is a fairly small amount when it comes to canning. Although I haven't tried it personally, you could most likely double or even triple the recipe as long as the contents of the pot don't go above the Instant Pot's max fill line.
Low FODMAP, Low Carb, Keto, Paleo, and Whole30
In addition to being low FODMAP, this salsa recipe is also suitable for the low carb, Keto, Paleo, Whole30, and vegan diets when eaten with compliant chips. Many salsa recipes add sweetener of some sort, usually refined sugar, but I didn't find that sweetener made this salsa taste any better. You are welcome to add sweetener per your own personal taste and dietary restrictions.

Spicy Food Warning
Although this salsa recipe is low FODMAP, it does contain jalapeños, red pepper flakes, and other spicy ingredients. Some people with IBS have poor reactions to spicy foods regardless if they are low in FODMAPs. Talk to your doctor or dietician with any concerns before making this salsa recipe.
Necessary Equipment
- 6-quart Instant Pot, 8-quart Instant Pot, or comparable electric pressure cooker
- Chopping board and knife
- Can opener (if using canned tomatoes)
- Citrus juicer
- Plastic spoon
- Air tight container
- Refrigerator
Low FODMAP Instant Pot Salsa: Ingredients & Success Tips
Garlic-infused olive oil
To add garlic flavor without the FODMAPs, I first add garlic-infused olive oil and sauté the peppers and leeks in garlic oil. This is another HUGE advantage to stewing the salsa as we can easily incorporate this garlicy flavor without the FODMAPs.
To start making this salsa recipe, I hit sauté on the Instant Pot. Once the display reads "Hot," I add the garlic-infused oil and swirl the pot to coat it in oil.
Green bell pepper and jalapeños
For peppers, I add green bell pepper and jalapeños. Containing the FODMAP fructans, green bell pepper is low FODMAP in servings of up to ½ cup or 75 grams. We're adding 1 ½ cups, about 1 large pepper, across 20 servings.
Jalapeños have been newly tested by Monash University fairly recently. According to Monash University's low FODMAP Diet App (from which all of the following FODMAP info is sourced), they've found them to contain fructose and list them as low FODMAP in quantities of up to 1 small chili or 29 grams per serving. We're only adding 68 grams total across 20 servings, coming to about 3.4 grams per serving. When combined with the tomatoes and red pepper flakes (discussed below) that also contain the FODMAP fructose, it is still below the tolerable amount per serving for low FODMAP.
Leeks
To add some oniony flavor without the traditional white onion, which is high FODMAP, I add some finely chopped leeks. The dark green leaves of the leek are low FODMAP in quantities of up to 1 cup or 100 grams per serving.
After adding the oil to the Instant Pot, I add the peppers and leeks and sauté for 3 minutes, stirring frequently.

Red pepper flakes
Then, to bring out the spicy flavor of the red pepper flakes, I add them to the pot and sauté for 30 seconds, stirring constantly. As written, I would consider this salsa to be medium spicy. If you prefer a milder salsa, feel free to lessen the amount of red pepper flakes. The quantity of jalapeño can also be reduced for less heat.
Red pepper flakes, listed as "chili flakes" in the Monash app, have been recently tested for FODMAPs. Containing the FODMAP fructose, they are listed as low FODMAP in servings of up to 1 teaspoon or 2 grams per serving. We are adding 1 teaspoon across 20 servings. When combined with jalapenos and tomatoes that also contain fructose, it is still well below the tolerable amount per serving.
Water, vinegar, and lime juice
Once I've sautéed the red pepper flakes for 30 seconds, I hit "Cancel" on the Instant Pot and slowly pour in water, white vinegar, and lime juice. The bottom of the pot shouldn't need scraping after the pot deglazes, but make sure to check for any stuck food on the bottom anyway, just in case.

I chose white vinegar with a minimum of 5% of acetic acid as the acid helps preserve the salsa longer. It is also the recommended threshold for canning (see my discussion above on whether or not this salsa is suitable for canning). White vinegar has been recently tested for FODMAPs by Monash University and is low FODMAP in quantities of up to 2 tablespoons or 42 grams per serving.
Lime juice adds refreshing brightness and further acidity to the salsa. Containing fructans, lime juice is low FODMAP in servings of up to 1 cup or 250 grams per serving. Although green bell pepper also contains fructans, these quantities across 20 servings do not even come close to exceeding the maximum tolerable amount per serving for low FODMAP.
Tomatoes
Quickly after adding the aforementioned liquids, I add tomatoes, either fresh common tomatoes or canned tomatoes, and their juices. If your fresh tomatoes are not very juicy, you may want to add additional water to the pot so that you don't get a burn error.
This salsa recipe is a great way to use up fresh garden tomatoes. Or, if you don't have fresh tomatoes or don't want to mess with them, you can also used canned diced tomatoes. I typically go with canned diced tomatoes as I don't grow my own. However, if you are eating low FODMAP and Keto, canned tomatoes contain slightly more carbs than fresh.
Common raw tomatoes have been recently retested by Monash University. Previously listed as FODMAP-free, common raw tomatoes are now listed as containing the FODMAP fructose and are low FODMAP at servings of up to ½ of a tomato or 65 grams per serving. We are adding about 450 grams across 20 servings, coming to only 22.5 grams per serving.
Also containing fructose, canned tomatoes are low FODMAP in servings for up to ½ cup or 100 grams per serving.
Scallions (a.k.a. green onions), green tops only
To add more oniony flavor without the traditional high FODMAP white onion, I add the chopped green tops of scallions (a.k.a. green onions), which are FODMAP-free. I don't sauté them in the beginning as they turn to flavorless mush when sautéed.
Seasonings
Finally, to season the salsa, I add the following herbs and spices:
- Dried chives - one of my favorite low FODMAP ingredients!
- Ground cumin
- Salt
- Pepper

Pressure Cook
Once all of the ingredients are added, I stir the contents of the pot, close the lid, set the pressure release valve to "Sealing," and set the timer for 5 minutes. I turn the "Keep Warm" button off.

Once the cooking cycle completes, I allow the pressure to release naturally for 10 minutes and then manually release the remaining pressure.
Cool and chill
Once the pressure has been released, I hope the Instant Pot lid and stir the salsa. I allow the salsa to cool in the Instant Pot, uncovered, for 10 minutes. Then, I transfer the salsa to an airtight container and refrigerate for a minimum of 4 hours but preferably overnight. It's a myth that you have to wait for food to cool completely before putting it in the refrigerator. If you want to use the salsa quickly, I recommend just cooling it at room temperature for 10 minutes and getting it in the fridge.
After the salsa has chilled in the fridge for 4 hours, I taste and adjust the seasonings, vinegar, and lime juice if needed. Keep in mind that the salsa will become more spicy and flavorful the longer it chills. The salsa you taste today may taste very different tomorrow.

Storage
I store this low FODMAP salsa in an airtight container in the refrigerator for up to 2 weeks. Again, if you want to can it, see my discussion on canning above.
What can I eat this low FODMAP salsa with?
This low FODMAP salsa can be enjoyed with the following Low FODMAP recipes:
Additionally, eat it with your favorite Mexican and Tex Mex dishes: tacos, burritos, nachos (using compliant tortilla chips), and more!
When eating low FODMAP and Keto, I use pork rinds as an easy Keto chip. They dissolve quickly when hit with the salsa, so you have to eat them quickly, but it's an easy low FODMAP and Keto chip option.

Chunky Low FODMAP Instant Pot Salsa
Ingredients
- 2 tablespoons garlic-infused olive oil
- 1 ½ cups green bell pepper, diced (about 1 large pepper)
- ½ cup jalapeño peppers, seeds removed, diced (about 2 medium peppers)*
- ½ cup leek, green tops only, finely-chopped
- 1 teaspoon red pepper flakes*
- ½ cup water
- ¼ cup white vinegar, minimum 5% acetic acid
- 3 tablespoons lime juice, freshly squeezed
- 3 cups fresh common tomatoes* and their juices, or 28 ounce can diced tomatoes and their juices
- ½ cup scallions, dark green parts only, chopped
- 1 tablespoon dried chives
- 1 ½ teaspoons ground cumin
- 1 ½ teaspoons salt
- ½ teaspoon pepper
Instructions
- Prepare ingredients: Prepare all ingredients per the list above before starting to cook.
- Sauté: Hit the “Sauté” button on your 6-quart Instant Pot, 8-quart Instant Pot, or comparable electric pressure cooker. Once the display reads “Hot,” add garlic-infused olive oil and swirl the Instant Pot to coat the bottom in oil. Add green pepper, jalapeno, and leeks and sauté for 3 minutes, stirring frequently. Add red pepper flakes and sauté for 30 seconds, stirring constantly. Hit “Cancel” on the Instant Pot.
- Add liquids and seasonings: Pour in water, vinegar, and lime juice and scrape the bottom of the pot clean with a plastic spoon if needed. Add tomatoes and their juices, scallions, dried chives, cumin, salt, and pepper and stir until combined.
- Pressure cook: Close the Instant Pot, set the pressure release valve to “Sealing” (if your model requires it), hit the “Pressure Cook” or “Manual” button, and set the timer for 5 minutes. Turn the "Keep Warm" button off.
- Naturally release pressure: Once the cooking cycle has completed, allow the pressure to release naturally for 10 minutes, and then manually release the remaining pressure.
- Cool and refrigerate: Open lid and stir salsa. Allow to cool in the Instant Pot, uncovered, for 10 minutes. Transfer to an airtight container and refrigerate for a minimum of 4 hours (preferably overnight) prior to eating. Stir, taste, and adjust seasonings, vinegar and/or lime juice as desired (see notes).
- Serve: serve with my Low FODMAP Instant Pot Salsa Chicken, as a topping on my Low FODMAP Instant Pot Carnitas, Low FODMAP Wet Burrito Bowls, low FODMAP tacos, nachos, or as a snack with compliant tortilla chips.
Notes
- FODMAPs: Please see "Low FODMAP Instant Pot Salsa: Ingredients & Success Tips" section in the post above for detailed FODMAP information pertaining to these ingredients.
- Spicy food warning: this low FODMAP salsa recipe contains spicy ingredients. Some people with IBS have problems with spicy food regardless of if its ingredients are low FODMAP.
- Spice level - as written, I would consider this low FODMAP salsa recipe to be about medium spicy. The amount of red pepper flakes and/or jalapeño can be lessened if you'd like to tone down the heat.
- Seasonings: the longer the salsa chills in the refrigerator, it becomes increasingly more spicy and flavorful. Keep that in mind when tasting and adjusting the seasonings and acids. Also, it tastes differently warm than it does chilled, so I wouldn't recommend doing a taste test until after it has chilled at least 4 hours.
- Tomatoes: If you use fresh tomatoes and they don't produce much juice when you chop them, you may want to add additional water (¼-1/2 cup) to the pot to avoid getting the dreaded burn error (dun dun DUN!).
- Servings: Produces about 5 cups or twenty ¼ cup servings.
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