Why Your Gut Reacts to Everything (And Why It’s Not Food Sensitivity)
If it feels like your gut reacts to almost everything you eat — even foods that used to feel safe — you’re not imagining it.
This is one of the most common (and distressing) experiences I hear from women:
“It feels like my body is attacking everything I put in it.”
After nearly 18 years as a Registered nurse, integrative health practitioner and holistic nutrition consultant and through having helped over 160 women work through gut issues, I want to reassure you of something important right away:
This is rarely because you’re intolerant to everything.
It’s usually because your immune system is on high alert.
And that distinction changes everything. Keep reading to learn more!
When the Gut Feels “Reactive,” the Immune System Is Usually Involved
Most women assume gut reactions mean:
food sensitivities
allergies
intolerance to specific foods
But in practice, what’s often happening is immune overactivation in the gut, not true intolerance.
The gut houses about 70–80% of your immune system. When the gut lining is compromised, the immune system becomes defensive — and it starts reacting to things it normally wouldn’t.
This is commonly referred to as leaky gut, but the term can feel vague or scary without context.
So let’s clarify what’s actually happening.
What “Leaky Gut” Really Means (Without the Fear)
Your gut lining is meant to act like a selective barrier:
nutrients pass through
pathogens stay out
the immune system remains calm
When that barrier is compromised:
partially digested food particles
bacterial fragments
toxins
can cross into circulation.
The immune system sees these as threats and rightly so, it mounts a response.
This doesn’t mean your gut is permanently damaged! It means it’s inflamed and overwhelmed.
Why the Immune System Starts Overreacting
Immune overactivation in the gut doesn’t happen randomly.
Common contributors include:
gut infections (candida, parasites, overgrowth of bad bacteria/sibo) or dysbiosis
chronic inflammation (lifestyle related)
prolonged stress physiology (adrenal/trauma)
poor digestion (low stomach acid, poor enzyme output)
repeated food restriction and reintroduction cycles
nutrient deficiencies that impair gut repair
Over time, the immune system becomes sensitized.
This is when women start saying:
“Even foods that are ‘healthy’ make me feel awful.” Some common culprits women react to include eggs, nuts/seeds, dairy and gluten.
Why it Feels Like Every Food is the Problem
When immune activation is high:
the gut loses tolerance
reactions become broader
symptoms feel unpredictable
This can look like:
bloating from foods you used to tolerate
pressure or distension regardless of what you eat
brain fog after meals
fatigue
skin reactions like excema, rosacea or psoriasis
joint pain or muscle aches
anxiety around food
The key point:
The immune system is reacting to these things because of gut permeability (leaky gut) — not because the specific food is bad for you.
That’s why cutting out more foods rarely fixes the issue long-term.
Why Elimination Diets Often Make This Worse
Elimination diets can be useful short-term — but when used repeatedly or aggressively, they often increase immune sensitivity.
Here’s why:
the immune system doesn’t learn tolerance
nutrient intake drops
gut repair slows
fear around food increases
reintroductions feel harder each time
Many women end up eating fewer and fewer foods, yet reacting more — not less.
That’s not because their gut is failing.
It’s because it’s stuck in protection mode.
The key to a healthy resilient gut is DIVERSITY of foods, and if you stay restricted for the long term - you’ll end up with a worse off gut enviroment and overall health. Restriction is never the answer!
The Role of Gut Infections and Dysbiosis
Gut infections and microbial imbalance are one of the most common drivers of immune activation, chronic digestive symptoms and food “sensitivites”.
When opportunistic bacteria or yeast dominate:
inflammation increases
the gut lining weakens
immune signaling escalates
This creates a vicious cycle:
Dysbiosis irritates the gut lining
Permeability increases
Immune reactions intensify
Symptoms expand
Until the gut environment changes, the immune system stays defensive.
Why “Healing Foods” Can Backfire in This Phase
Many women try to heal their gut by adding:
more fiber
raw vegetables
fermented foods
“superfoods”
But when the immune system is already activated, more stimulation isn’t better.
High-fermentable foods can:
increase gas and pressure
worsen bloating
amplify immune reactions
This doesn’t mean those foods are bad! It means the gut isn’t ready for them yet.
The Importance of Phases in Gut Healing
One of the biggest mistakes I see is women skipping straight to rebuilding the gut (for example drinking bone broth or probiotics first) — without first calming the immune response or lowering inflammation in the body. This means looking at WHAT is driving the underlying issues - bloating, gas, IBS type symptoms, constipation etc and also looking at how the digestive system is functioning as a whole (enzymes, acids, bile flow).
Gut healing must then happen in phases based on testing with functional lab testing like we do inside The Happy Gut Root Cause Reset program:
Phase 1: Calm and Stabilize
reduce immune triggers
support digestion
lower inflammation
simplify food choices
Phase 2: Discover the root cause/Repair the Gut Lining
Uncover whats happening in the microbiome via a functional GI MAP stool test
Provide specific nutrients for regeneration
Improve barrier integrity
Phase 3: Thrive, Rebuild and Reintroduce
implement daily lifestyle habits that keep your gut microbiome healthy and resilient
diversify the microbiome with a variety of foods/expand food tolerance now that the microbiome is balanced and gut lining supported
When these phases are skipped or rushed, symptoms persist — even with “good” or healthy foods. These are the three phases we take women through inside our 6 month program, you can read more about it here.
Why This Is Especially Common in Perimenopause
Hormonal shifts in perimenopause can:
reduce immune tolerance
increase inflammatory signaling
slow gut repair
make reactions feel more intense
This is why many women say:
“My gut just changed in my 40s.”
The vulnerability was often already there, hormones fluctuating simply accentuated the issue.
What This Means (And What It Doesn’t)
Let’s be very clear:
This does not mean:
you’re allergic to everything
you need to restrict forever
your gut is permanently damaged
food is the enemy
It does mean:
your immune system needs calming
your gut lining needs support
healing needs structure, not force
Tolerance to a wide variety of foods is done not by avoidance, but by repair and restoration of the gut-immune pathway.
In Short
When the gut lining is compromised, the immune system overreacts.
This creates the illusion of “reacting to everything.”
The issue isn’t the food — it’s immune activation (we can measure this in testing we run).
When the immune response is calmed and the gut barrier is restored, food tolerance returns.
What to Do Next
If your gut feels reactive no matter what you eat — especially alongside bloating, fatigue, or food anxiety — it may be time to stop chasing foods and start addressing the root cause.
Book a free 30 Min Root Cause Assessment Call here so that we can discuss whether the Happy Gut Root Cause Reset Program could help you resolve your symptoms, for good.
