Is Your Diet Damaging Your Gut? The Hidden Dangers of High-Protein, High-Fat Diets
Why keto, carnivore, and even strict paleo might be doing more harm than good to your microbiome.
High-protein, high-fat diets like keto and carnivore have exploded in popularity over the last decade, promising everything from weight loss and mental clarity to better blood sugar control. And while some people experience short-term success, what’s often overlooked is the long-term impact these diets can have on your gut health, specifically your microbiome.
If you’ve been following one of these diets (or are considering it), it’s time to take a closer look at how they affect your digestive system and why your gut might be paying the price.
The Microbiome Needs Plants. Period.
Your gut microbiome is made up of trillions of bacteria that play a major role in digestion, immunity, hormone regulation, and even mental health. These bacteria feed primarily on fiber, especially prebiotic fibers found in fruits, vegetables, whole grains, legumes, and seeds.
Keto and carnivore diets drastically limit or completely eliminate these plant foods, which starves your beneficial gut bacteria over time. The result?
Reduced microbial diversity
Increased gut inflammation
Higher susceptibility to leaky gut, IBS, and constipation
Even paleo, which allows some plant foods, often falls short in providing enough diverse fiber sources to maintain a resilient microbiome long term.
Too Much Fat Can Disrupt Gut Balance
While healthy fats are important, diets that heavily emphasize fat (especially saturated fat) can change the makeup of your gut bacteria in unfavorable ways. Studies show high-fat diets may:
Increase endotoxins (harmful compounds that leak into the bloodstream)
Promote the growth of inflammatory gut microbes
Contribute to symptoms like bloating, gas, and sluggish digestion
And when protein is added to the mix, particularly animal-based protein with little to no fiber, the risk of gut dysbiosis grows.
What About Weight Loss?
Yes, many people lose weight initially on these diets. But if that weight loss comes at the cost of a weakened gut, it often backfires. I regularly work with clients who come to me after months or years on high-protein, high-fat diets feeling worse than when they started:
Chronic bloating
Fatigue
Skin issues
They’ve hit a wall, and their microbiome is often the missing piece.
Your Gut Wasn’t Meant to Live Without Carbs
Carbohydrates have been unfairly demonized in mainstream diet culture. But the right carbs—think sweet potatoes, berries, lentils, oats, and quinoa—are not your enemy. They're essential for:
Feeding good gut bacteria
Producing short-chain fatty acids (like butyrate) that reduce inflammation
Supporting a healthy gut lining
Promoting regularity
When we cut out carbs, we’re not just skipping sugar. We’re depriving our gut of vital nutrients that help it function.
A More Balanced Approach to Gut Health
This doesn’t mean you need to go vegan overnight. But it does mean rethinking restrictive eating patterns that cut out entire food groups, especially plant foods. A gut-friendly diet should focus on:
A wide variety of colorful fruits and vegetables
Plenty of plant-based fibers
Moderate protein from both animal and plant sources
Healthy fats in balanced amounts
And most importantly, diversity in what you eat and what your gut bacteria have to work with
Final Thoughts: It's Not Just About What You Take Out. It's What You Feed.
Your gut thrives on balance. While keto or carnivore may seem like quick fixes, they often come with hidden costs, especially when it comes to your long-term gut health. Before you cut carbs or pile on more protein, ask yourself: What is my gut missing?
Let's Create a Gut Plan That Actually Works
If you’ve been following a restrictive diet and still feel bloated, fatigued, or stuck, it’s time to look beneath the surface. As a Functional Nutritional Therapy Practitioner based in Eugene, Oregon, I help clients repair their gut and rebalance their microbiome with real food, not fads.
Whether you’re coming off keto or just starting to question what’s working for your body, I’ll meet you where you are and help you build a sustainable plan that supports your gut and your overall wellness.
Reach out today to schedule your free discovery call. Let’s find a gut-healing strategy that supports your health for the long haul. https://nicolejoycehealthcounseling.com/contact OR 541-914-9147