What "Bad" Foods Are Good for Your Gut?
Written by: Vincent Pedre M.D. | February 12, 2024 | Time to read 10 min
For years, certain foods have been unfairly demonized as "bad" for your health—whether due to their fat content, sugar levels, or potential digestive irritants.
In the 1980s, we were sold a lie—that fat was the ultimate villain behind heart disease, obesity, and every health woe imaginable. The food industry and so-called “experts” waged war on fat, flooding the market with low-fat, fat-free garbage loaded with—you guessed it— sugar.
Meanwhile, the sugar industry sat back and laughed, quietly funding research to keep the spotlight off their sweet little secret. And what happened?
As a result, food companies replaced fat with refined sugars and processed carbohydrates to maintain flavor, fueling a massive spike in obesity, diabetes, and metabolic disorders. Today, 1 in 3 children are at risk of becoming diabetic by their teenage years.
Ironically, while we avoided fat, we unknowingly consumed more sugar than ever, proving that the real culprit wasn’t fat—but the ultra-processed, sugar-laden foods that took its place.
We got fatter, sicker, and more addicted to sugar than ever. But hey, at least we weren’t eating butter, right? Wrong.
But here’s the surprising truth: Some of these so-called villains can actually benefit your gut microbiome—that community of trillions of bacteria that influence digestion, immunity, and even mood. The gut microbiome plays a critical role in digestion, immunity, and overall well-being. By nurturing this ecosystem, we can enhance nutrient absorption, reduce inflammation, and improve digestion.
It’s not just what you eat, but how your body interacts with it. Some of these so-called "bad" foods actually nourish your gut bacteria, providing probiotics, fiber, and essential nutrients that support digestion and overall wellness. So let’s set the record straight.
Here are 10 foods you may have been avoiding that can actually be gut-friendly superstars.
[But First] How Your Gut REALLY Works
What Is the Gut Microbiome?
The gut microbiome is a collection of trillions of microorganisms residing in our digestive tract. These microbes influence everything from digestion and nutrient absorption to mental health and immune function. A balanced gut microbiome consists of diverse bacteria strains, including beneficial probiotics and fiber-digesting microbes.
A healthy microbiome is essential for breaking down food, producing essential vitamins, and even regulating mood through the gut-brain axis. Research has shown that individuals with a diverse microbiome tend to have better overall health, weight, and digestion compared to those with an imbalanced gut. Learn more about gut health basics here.
How Do Certain "Bad" Foods Benefit Gut Health?
Many foods that have been labeled as unhealthy are actually rich in fiber, polyphenols, probiotics, or prebiotics. These compounds help feed good bacteria, promote digestion, and support a balanced microbiome. When consumed in their least processed forms, these foods can provide significant gut health benefits.
Some of these foods may have been demonized due to misinformation or outdated dietary advice. For instance, high-fat dairy has been discouraged due to saturated fat content, but research suggests that full-fat fermented dairy is beneficial for diversifying gut bacteria. Similarly, coffee has been criticized for its acidity, yet its polyphenol content supports gut health.
Top "Bad" Foods That Are Actually Good for Your Gut
1. Full-Fat Dairy (Cheese, Yogurt, Kefir)
❌ Why It’s Considered "Bad": High in saturated fat and lactose.
✅ Why It’s Good for Your Gut: Fermented dairy (think yogurt, kefir, and aged cheeses) is loaded with probiotics —the good bacteria that support digestion and gut balance. Plus, full-fat dairy is often easier to digest and better tolerated than its low-fat counterpart, which can contain added sugars and stabilizers that disrupt gut health.
Gut Tip: If you’re lactose-sensitive, try kefir—it has enzymes that help break down lactose, making it easier on digestion.
2. Chocolate
❌ Why It’s Considered "Bad": High in sugar and calories. Milk chocolate can aggravate food sensitivities in individuals that are dairy sensitive.
✅ Why It’s Good for Your Gut: Choose right, choose dark chocolate! It’s rich in polyphenols — plant compounds that act as prebiotics —feeding beneficial gut bacteria like Lactobacillus and Bifidobacterium. You can read more about the secret gut health benefits of dark chocolate in my full blog post here — The Shocking Reason to Eat More Chocolate .
Gut Tip: Go for 70% cocoa or higher to get the gut-boosting benefits while minimizing sugar. Read labels. Choose a dark chocolate sweetened with allulose for greater health benefits (see below).
3. Coffee
❌ Why It’s Considered "Bad": Too acidic and irritating to digestion. It causes jitters and acid reflux.
✅ Why It’s Good for Your Gut: Coffee contains polyphenols and soluble fiber that feed your good gut bacteria. It stimulates gastric motility, keeping things moving and preventing constipation. And if you want the best low-acid organic coffee, that is easy on your stomach, and third-party tested for purity try Happy Gut Coffee right here. Plus, the polyphenols and antioxidants in coffee can help nourish beneficial gut bacteria, reducing inflammation and promoting overall digestive well-being. To learn more about how coffee’s antioxidants can boost your gut health, click here.
Gut Tip: If coffee bothers your stomach, try a cold brew —it’s lower in acidity (and higher in caffeine) but still packed with gut-friendly antioxidants.
4. Butter
❌ Why It’s Considered "Bad": Demonized during the anti-fat movement of the late 20th century, butter was made the villain in heart disease. Non-grass-fed butter contains toxins, hormones, pesticides, and inflammatory omega-6 fats from grain-fed cows, which can disrupt gut health and contribute to inflammation and digestive issues.
✅ Why It’s Good for Your Gut: Grass-fed butter is gut-friendly due to CLA (conjugated linoleic acid) and butyrate, which reduce inflammation, strengthen the gut barrier, and support beneficial bacteria. CLA also aids metabolism and helps prevent digestive issues like leaky gut, making butter a powerful ally for gut health.
Gut Tip: If you're dairy-sensitive but want the gut-friendly benefits of butter, try using ghee instead! Ghee is clarified butter, meaning it has been filtered to remove lactose and casein, the two compounds in dairy that often trigger digestive issues. It still retains all the gut-nourishing nutrients found in grass-fed butter, like CLA and butyrate. Plus, ghee is easier to digest and more stable for high-heat cooking, making it a great alternative for those with mild dairy intolerances.
5. Pickles & Fermented Vegetables (Sauerkraut, Kimchi)
❌ Why It’s Considered "Bad": High in sodium. High in histamines, which can trigger allergic reactions, headaches, skin issues, or digestive discomfort in people with histamine intolerance.
✅ Why It’s Good for Your Gut: Naturally fermented pickles and veggies are full of probiotics that support digestion, immunity, and gut microbiome diversity. A more diverse gut microbiome supports lower inflammation.
Gut Tip: Look for unpasteurized versions (found in the refrigerated section or at your local farmer’s market) to ensure they still contain live beneficial bacteria.
6. Potatoes (Especially When Cooled)
❌ Why It’s Considered "Bad": High in carbs and starch.
✅ Why It’s Good for Your Gut: Cooked then cooled potatoes contain resistant starch, a special type of fiber that feeds beneficial gut bacteria and supports digestion.
Gut Tip: Cook your potatoes, let them cool, and enjoy them as potato salad or roasted leftovers for a gut-friendly meal.
Alternative Superfood: If you don’t want to eat regular potatoes, go for these, instead. Purple potatoes are a gut-friendly powerhouse thanks to their high content of resistant starch and antioxidants. Additionally, the anthocyanins (powerful antioxidants) in purple potatoes help lower gut inflammation, support microbiome diversity, and protect against oxidative stress. For maximum resistant starch benefits, cook purple potatoes and let them cool before eating —this increases their resistant starch content, making them even better for gut health!
7. Sourdough Bread
❌ Why It’s Considered "Bad": Contains gluten, and if you follow me you know that our over-glutened bread is responsible for so much of the gut disruption and gut-related health disorders we are seeing in the U.S.
✅ Why It’s Good for Your Gut: The fermentation process used in making traditional sourdough bread (72 hours total) breaks down gluten, making it easier to digest while also providing beneficial bacteria. Plus, it has a lower glycemic index than regular bread. Discover our gut-friendly recipes here.
Gut Tip: Look for authentic sourdough made using traditional fermentation (not the fast-yeast versions found in most grocery stores). For a more gut-friendly, lower-gluten sourdough, try using Einkorn wheat instead of modern wheat. Einkorn is an ancient grain with a more delicate gluten structure, making it easier to digest and less likely to trigger inflammation or gluten sensitivities. If you do, expect a slightly denser, nutrient-rich loaf!
8. Beer & Wine (In Moderation)
❌ Why It’s Considered "Bad": Alcohol disrupts the gut microbiome by killing beneficial bacteria, increasing gut permeability (leaky gut), causing inflammation, and promoting the overgrowth of harmful microbes, which can lead to digestive issues, immune dysfunction, and systemic inflammation.
✅ Why It’s Good for Your Gut: Red wine contains polyphenols, which feed beneficial gut bacteria. Certain beers, especially unfiltered varieties, contain probiotic-friendly yeasts and B vitamins that can support gut health. Some studies suggest that moderate consumption of polyphenol-rich beers (like dark beers or craft ales) can support gut bacteria diversity.
Gut Tip: Stick to one glass of wine or beer once a week (max) with a meal to minimize any potential negative effects on gut bacteria. Or opt for a non-alcoholic, unfiltered, or naturally fermented beer, which may offer some gut-friendly compounds without the harmful effects of alcohol.
9. Spicy Foods (Chilies, Peppers)
❌ Why It’s Considered "Bad": Spicy foods can irritate the digestive tract's lining and trigger inflammation, leading to increased gut sensitivity and discomfort.
✅ Why It’s Good for Your Gut: The active compound capsaicin in spicy foods has been shown to increase gut bacteria diversity and even stimulate digestion. Although not a study, a friend swears he fixed his gut issues (possibly a parasite) by eating spicy foods for one month. This is not scientific, and should not be used as therapy. Find solutions to digestive issues in our blog category here.
Gut Tip: If spicy foods upset your stomach, pair them with a healthy fat (like avocado or olive oil) and a resistant starch (like cooked and cooled white rice) to soothe digestion.
10. Certain Sugar Substitutes (Stevia, Monk Fruit, etc.)
❌ Why It’s Considered "Bad": Artificial sweeteners can disrupt gut bacteria.
✅ Why It’s Good for Your Gut: While some sweeteners (like aspartame) negatively impact gut bacteria, natural alternatives like stevia and monk fruit do not. They can help satisfy your sweet tooth without disrupting gut health. Allulose, a low-calorie rare sugar derived from dates, corn, maple syrup, figs, and raisins through an enzymatic process that converts fructose into allulose, activates GLP-1 receptors by stimulating hormone release in the gut, slowing digestion, reducing appetite, improving insulin sensitivity, stabilizing blood sugar, and promoting fat metabolism, making it a powerful natural aid for weight loss.
Gut Tip: Avoid sweeteners ending in "-tol" (like sorbitol and maltitol), which can cause severe bloating in some people. Read labels. Don’t trust if a product says sugar-free. Find out what sugar substitute is being used in bars, powders, and other dessert look-alike substitutes.
How to Incorporate These Foods into a Gut-Healthy Diet
✅ Choose the Right Versions
Opt for fermented dairy over highly processed versions.
Pick dark chocolate (70%+ cocoa) instead of milk chocolate.
Go for natural sourdough instead of processed white bread.
✅ Pair Foods for Maximum Gut Benefits
Combine prebiotic-rich foods (like bananas, onions) with probiotic foods (like yogurt, kefir) for a synergistic gut boost.
Use healthy fats like olive oil for flavor or ghee for high-heat cooking, which also provides gut-nourishing butyrate.
✅ Avoid Processed Versions
Stick to homemade sauerkraut and pickles instead of store-bought versions loaded with preservatives.
Choose whole, unprocessed, organic potatoes instead of refined potato products.
Rethinking "Bad" Foods
The idea that certain foods are "bad" for your health is often an oversimplification. In reality, many of these so-called villains actually support your gut —as long as they’re consumed in their least processed forms and in the right way.
So instead of fearing these foods, embrace them mindfully. Your gut bacteria will thrive, your digestion will improve, and you’ll feel better overall. Food is not the enemy—it’s about balance, quality, and how it interacts with your unique microbiome.
In my book, The GutSMART Protocol, I’ve created a 14-day personalized gut-healing plan tailored to your gut type, based on a quiz I call the GutSMART Quiz.
Ready to take your digestion and gut health to the next level? Take the FREE GutSMART Quiz to find out your gut type. With GutSMART Score in hand, we'll let you know what foods are in, and which ones are a no-go, for a healthier overall gut, body and mind.
Ready to start nourishing your gut the right way? Your digestive system (and your overall health) will thank you! 💚
