Gut-Healthy Grocery List: What to Eat for a Happier Microbiome

November 05, 2025

You can read everything there is about gut health and the microbiome, but if you don’t know what to buy at the grocery store, it’s hard to turn that knowledge into action.

If you’ve ever been confused about which foods actually support a healthier gut, this grocery guide breaks down exactly what to add to your cart to keep your microbiome happy.

Your Ultimate Gut-Healthy Grocery List

There are five main categories of gut-friendly foods to keep an eye out for at the grocery store: foods rich in prebiotics, probiotics, fiber, polyphenols, and omega-3s.

These foods help nourish your gut bacteria, support digestion, and contribute to overall health. Let’s take a closer look at these categories and what to buy from each:

Prebiotic-Rich Foods

Prebiotics are special types of fiber that feed the good bugs in your gut—think of them as fertilizer for your microbiome. Eating prebiotic foods regularly can help increase the diversity and resilience of your gut bacteria.

Some of the most common prebiotics include inulin, FOS (fructooligosaccharides), GOS (galactooligosaccharides), beta-glucan, and resistant starch.

These prebiotics are fermented by your gut bacteria to produce short-chain fatty acids (SCFAs), which help reduce inflammation, strengthen your gut lining, and improve digestion.

The top prebiotic-rich foods to add your grocery cart include:

Garlic: Rich in inulin and FOS
Onions: Contain inulin and FOS
Leeks: A great source of inulin
Asparagus: Contains inulin
Green (less ripe) bananas: Provide resistant starch
Oats: A good source of beta-glucan
Apples: Contain pectin
Jerusalem artichokes: High in inulin
Chicory root: One of the richest natural sources of inulin

Probiotic-Rich Foods

Many people know probiotics are good for your gut, but what exactly are they? While prebiotics feed your gut bacteria, probiotics are the live, healthy bacteria themselves.

These beneficial microbes do much more than help with digestion—they also support your mood, metabolism, brain function, heart health, and immune system.

The best way to get probiotics from your grocery store is through fermented foods. These foods have been naturally fermented, allowing the growth of live bacteria that can help support your microbiome.

Here are some of the probiotic foods you might find at your grocery store:

Sauerkraut: Fermented cabbage
Kimchi: Korean fermented cabbage with spices
Fermented pickles: Look for naturally fermented, not pasteurized
Yogurt: Must say “contains live and active cultures” on the label
Kefir: Fermented dairy drink, similar to drinkable yogurt
Tempeh: Fermented soybean cakes
Miso: Fermented soybean paste
Kombucha: Fermented tea
Natto: Fermented soybeans, popular in Japanese cuisine, great source of probiotics and vitamin K2
Some types of fermented cheeses: Like aged gouda, Swiss, and cheddar (look for raw or unpasteurized versions)
Water kefir: A dairy-free fermented drink alternative to regular kefir

High-Fiber Foods

While prebiotics are a special type of fiber, other types—like soluble and insoluble fiber—also play important roles in gut health.

Soluble fiber dissolves in water, helping to soften stool and support healthy digestion.

Insoluble fiber doesn’t dissolve in water but adds bulk to your stool, helping keep things moving and clearing out toxins.

Why Does Fiber Matter?

Most people don’t get nearly enough fiber. The average American eats only 7-10 grams per day, while the recommended intake is 28 grams for women and 35 grams for men.

Fiber not only helps keep digestion regular but also feeds your gut bacteria, helping them thrive and produce beneficial compounds like short-chain fatty acids.

These compounds help reduce inflammation, strengthen your gut lining, and support immune health. Plus, fiber can help you feel fuller longer, which supports healthy weight management.

Here are some of the highest-fiber foods to add to your grocery cart:

Beans and Legumes: Chickpeas, lentils, split peas, black beans, kidney beans, white beans, etc.
Whole Grains: Quinoa, barley, oats, bulgur, amaranth, brown rice, whole wheat bread
Fruits: Raspberries, blackberries, pears, avocado, kiwi
Vegetables: Artichokes, green peas, broccoli, kale, Brussels sprouts
Nuts and Seeds: Chia seeds, flax seeds, almonds

Adding a variety of fiber-rich foods to your diet is a great way to get a balance of soluble and insoluble fibers that support your gut health.

Polyphenols

Polyphenols are a subclass of antioxidants found naturally in plant foods, especially fruits, vegetables, herbs, spices, tea, coffee, and wine.

By fighting oxidative stress and inflammation, polyphenols support several key systems in the body, including your gut.

Certain red and purple-colored polyphenols—like anthocyanins and ellagitannins—are especially effective at supporting gut health by feeding beneficial bacteria and reducing inflammation in the gut.

Other polyphenols include flavonoids, phenolic acids, stilbenes, and lignans.

Here are some of the top gut-loving polyphenols and where to find them:

Raspberries, strawberries, and blackberries: Rich in anthocyanins and ellagitannins
Blueberries: Rich in anthocyanins
Pomegranate: Packed with ellagitannins, including punicalagins—a unique ellagitannin that promotes beneficial gut microbes and is converted by gut bacteria into urolithin A, a metabolite linked to gut and cellular health.
Apples: High in fiber and flavonoids like quercetin and catechin, especially in the skin.
Cherries: Contain anthocyanins
Red grapes: Source of resveratrol and flavonoids
Beets: Contain betalains (antioxidant pigments chemically different from polyphenols) and fiber to help digestion
Red cabbage: Rich in anthocyanins
Coffee: Loaded with phenolic acids
Dark chocolate: Contains flavonoids and flavanols like epicatechin and catechin
Green tea: Rich in catechins, a powerful type of flavonoid
Herbs and spices: Turmeric (curcumin), rosemary, cinnamon, and cloves are all rich in different polyphenols

Healthy Fats and Omega-3s

Healthy fats are essential for a strong and thriving gut. Certain types of fats—especially omega-3 fatty acids—help calm inflammation in the gut, strengthen the gut barrier, and support gut microbial balance.

Some of the healthiest fats to shop for include:

Extra-virgin olive oil: Rich in monounsaturated fats and antioxidants like oleic acid and oleocanthal
Avocados and avocado oil: Packed with heart-healthy fats and fiber
Fatty fish: Salmon, sardines, mackerel, and anchovies are excellent sources of anti-inflammatory omega-3s
Flaxseeds: A vegan source of omega-3s, though less bioavailable than those from marine sources

Shopping Tips for a Microbiome-Friendly Cart

If you’re unsure what to look for on labels, here are some quick tips to help you choose gut-friendly foods at the grocery store:

Look for “live and active cultures” on yogurt labels. This means the yogurt contains beneficial probiotics that can support your gut.
Avoid pasteurized fermented foods if you want probiotics. Pasteurization kills live bacteria, so probiotic-rich fermented foods are usually found only in the refrigerated section.
Choose whole grains over refined grains. Whole grains contain more fiber, which feeds your gut bacteria and supports digestion.
Check ingredient lists for added sugars and preservatives. These can disrupt your gut microbiome, so opt for minimally processed foods whenever possible.
When buying pickles or sauerkraut, look for labels that say “naturally fermented.” Avoid vinegar-based or shelf-stable versions, as they don’t contain live probiotics.

Key Takeaways

Feed your gut bacteria with a mix of prebiotic fibers from foods like garlic, onions, and green bananas.
Add probiotics by choosing fermented foods such as yogurt, sauerkraut, kimchi, and kombucha.
Don’t forget fiber! Aim for a variety of soluble and insoluble fibers from beans, whole grains, fruits, and vegetables.
Load up on polyphenols, as these antioxidant-rich compounds found in berries, coffee, green tea, and spices support gut health and reduce inflammation.
Include healthy fats and omega-3s from sources like olive oil, avocados, fatty fish, and flaxseeds to calm gut inflammation and strengthen your gut lining.

Improving your gut health doesn’t have to be complicated. Start by adding just one or two of these foods to your cart this week—you’ll feel the difference!

Author: Cambria Glosz, Registered Dietitian

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