The ‘Gut-First’ Healing Myth: Why Some People Need to Fix Their Nervous System Before Their Microbiome
If you’ve spent any time in the world of health and wellness, you’ve probably heard the golden rule: "All health starts in the gut." It’s practically a mantra at this point. Got bloating? Heal your gut. Feeling sluggish? Heal your gut. Bad skin, brain fog, anxiety, joint pain? You guessed it, heal your gut.
And listen, I get it. As a functional medicine doctor, I love a good gut protocol as much as the next person. I’ve seen firsthand how powerful microbiome support can be. But what if I told you that for some people, the gut isn’t actually the root problem? What if those gut issues you’ve been battling aren’t even starting in your gut?
Cue the plot twist: For many people, the real issue is a dysregulated nervous system.
Yep, I said it. Sometimes, no matter how many probiotics you pop, how much bone broth you sip, or how religiously you cut out gluten and dairy, your gut just won’t heal, because it’s stuck in a state of stress. And if your nervous system is running the show in fight-or-flight mode, your gut is just along for the chaotic ride.
So today, let’s bust the myth that gut health is always the first step in healing and talk about why, in some cases, you need to fix your nervous system before your microbiome even stands a chance.
The Gut-Brain Axis: A Two-Way Street
You’ve probably heard of the gut-brain axis—the connection between your gut and your nervous system. What a lot of people don’t realize, though, is that this relationship is a two-way street.
It’s not just your gut affecting your brain (though that’s a thing). Your nervous system can actually dictate how your gut functions. And when the nervous system is in a state of constant stress, digestion takes a backseat.
The vagus nerve (your body’s main relaxation switch) controls digestion, but if you’re stressed, it’s like someone cut the power to that system. Instead of efficiently breaking down and absorbing nutrients, your digestive system slows to a crawl, leaving you bloated, constipated, or running to the bathroom at the worst possible moments. PMCID: PMC5127403
Chronic stress also slows down or even shuts off digestive enzyme production—those little biochemical powerhouses that break down proteins, fats, and carbs into absorbable nutrients. Without enough enzymes, your food just sits there, fermenting and causing bloating, discomfort, and nutrient malabsorption. So you could be eating the healthiest, most nutrient-dense diet on the planet, but if your enzymes aren’t doing their job, your body isn’t actually getting the benefits. PMID: 37756251
In addition to this, your gut lining is supposed to be a strong yet selective barrier, allowing nutrients in while keeping harmful bacteria and toxins out. But chronic stress weakens this defense system, making the gut lining more permeable, a phenomenon often called “leaky gut.” This means that undigested food particles and inflammatory compounds can slip through into the bloodstream, triggering immune reactions, inflammation, and a growing list of food sensitivities.
If you’re constantly anxious, overwhelmed, or in survival mode, your gut isn’t getting the memo that it’s safe to function normally. Instead, it’s stuck in defense mode, leading to bloating, constipation, diarrhea, and a host of other “gut problems” that actually started in the brain.
This is why some people never fully heal their gut! Because they’re so focused on probiotics and elimination diets, they’re missing the real problem.
Signs Your Nervous System, Not Your Gut, is the Problem
So how do you know if your gut issues are actually a nervous system problem in disguise? Here are some red flags:
You’ve tried every gut protocol under the sun, but nothing seems to work long-term.
Your symptoms flare up during stressful times, even when your diet stays the same.
You have trouble digesting food, but your stool tests and labs don’t show major imbalances.
Your food intolerances keep multiplying. One day it’s gluten, then dairy, then suddenly almonds and avocado are giving you trouble, too.
You’re dealing with cold hands and feet, shallow breathing, anxiety, or chronic tension (all signs your nervous system is stuck in overdrive).
You can’t seem to relax, even when you’re supposed to be resting.
If this sounds familiar, your gut might be more of a victim in this situation than the true culprit.
Fixing the Nervous System First: Where to Start
So if gut healing isn’t working, what can you do? The answer isn’t another round of antimicrobials or stricter food rules. It’s nervous system regulation. Here are some of my favorite ways to shift your body out of stress mode and into healing mode:
1. Vagus Nerve Activation
Your vagus nerve is like the “chill button” for your gut. Activating it can improve digestion, reduce inflammation, and help your gut heal. Try:
Slow, deep belly breathing (inhale for 4, exhale for 8).
Humming, singing, or gargling (yes, gargling—think of it as a weird but effective nervous system workout).
Cold exposure (like splashing your face with cold water or ending your shower with a cold rinse).
2. Getting Out of Fight-or-Flight Mode
If your body constantly thinks it’s being chased by a tiger, digestion isn’t going to work. Start sending safety signals to your nervous system with:
Gentle movement (walks, stretching, NOT high-intensity workouts if you’re already burnt out).
Slow, mindful meals (put down your phone, chew your food, and actually enjoy your meals).
Tactile grounding techniques (like weighted blankets, warm baths, or even petting a dog).
3. Reframing Food Fear
If you’re constantly stressing about what you should or shouldn’t eat, your nervous system is staying in fight-or-flight mode making digestion worse. Start trusting your body again instead of overanalyzing every bite.
4. Balancing Circadian Rhythms
Your gut and nervous system are deeply tied to your light exposure and sleep patterns. Morning sunlight, less screen time at night, and a solid sleep schedule can do wonders for your gut-brain connection.
Now, I’m not saying gut protocols are useless—far from it! But they work best when your nervous system is in a regulated state. Once you’re out of chronic fight-or-flight mode, THEN things like probiotics, gut-healing nutrients, and dietary tweaks actually have a chance to work.
Conclusion
If you’ve been throwing everything at your gut—elimination diets, supplements, probiotics—with little success, it might be time to take a step back. Instead of asking, What’s wrong with my gut? try asking, Is my body even in a state that allows healing to happen?
Because here’s the truth: your gut can’t fully heal if your nervous system is stuck in fight-or-flight mode. No amount of probiotics will override chronic stress, poor vagal tone, or a dysregulated system that doesn’t feel safe enough to digest, absorb, and repair.
So before you jump into another round of gut protocols, start by supporting your nervous system. If this all sounds overwhelming, or if you’re wondering how to know what your body needs, let’s chat. I help clients navigate exactly this: uncovering what’s holding them back from real healing and creating a personalized plan that actually works.
Book a discovery call today, and let’s get to the real root of your gut issues so you can finally start feeling better.