🦠 Why Gut Issues Return After a Cut (And Why It’s Not the Carbs)

If you’re finishing a fat loss phase and suddenly feel like your digestion is worse—bloating, gas, constipation, food sensitivities flaring up—you’re not crazy. But let’s be very clear: this is not a sign that carbs are the problem. It’s a sign that your gut—and your entire body—is still in a malnourished state.

I see this all the time with clients. They’ve been cutting for 4–6 weeks, running on lowered energy availability, and the minute we start refeeding or adding carbohydrates back in, gut issues resurface. Their first instinct? “The carbs are causing it.” I hear the panic:

“It must be the sourdough.”
“I’m feeding candida again.”
“I think I need to go back to keto.”

No. Let’s break this down.

🧬 Cutting Starves the Gut—Literally

A cut isn’t just a reduction in energy. It’s a drop in micronutrients, fiber, fermentable substrates, and metabolic signals like T3. It’s a famine state. And guess who else goes hungry?

Your gut bacteria.

During a cut, your beneficial microbes—the ones that keep pathogens in check and maintain the gut lining—get underfed. And when that happens, two things start to unravel:

1. The mucosal barrier thins.

2. The immune system downregulates.

3. Digestion slows down—because the body shunts energy toward more essential systems like the brain, heart, and muscles, leaving less fuel for enzyme production, bile flow, and peristalsis.

This creates an opening for pathogenic or opportunistic microbes to sneak in or re-establish dominance. So when you reintroduce carbs—especially fermentable ones—you might feel worse not because you’re feeding the “bad bugs,” but because you’re finally feeding the good ones, and they’re trying to reclaim territory.

That process? It’s called die-off. Or more accurately: a Herxheimer reaction.

⚔️ Die-Off ≠ Overgrowth

Die-off symptoms—fatigue, mood swings, bloating, skin flares, weird body odor, changes in bowel movements—often mimic what people assume are “overgrowth” symptoms. But this isn’t a sign of fungal relapse or bacterial disaster. It’s a war. And the good guys are winning.

When you increase carbohydrates, especially after a long period of underfeeding, you:

• Reawaken dormant digestive fire (T3 rises)

• Stimulate bile and enzyme production

• Feed SCFA-producing bacteria (SCFA = short-chain fatty acids, like butyrate and acetate, which strengthen the gut lining, reduce inflammation, and improve motility)

• Starve out methane-producing archaea and sulfate-reducing bacteria by increasing gut movement

Yes, this process is uncomfortable. But it is necessary for long-term gut repair.

🥖 Not All Carbs Are Created Equal (Especially After a Cut)

A huge mistake I see? Clients try to reintroduce the same types of carbs they thrived on at maintenance—sourdough, white rice, salads, berries with seeds, potato skins, cassava, even sprouted oats or whole fruits with lots of fiber. But post-cut digestion is fragile. T3 is still suppressed, enzyme output is low, and motility is sluggish.

What digests well at maintenance might wreck you during refeed.

This is not a sign that you’re broken. It’s a sign to shift strategy.

🍯 The Best Carbs for Gut Repair (Refeed Edition)

Your digestion during a refeed is not “normal.” It is compromised, sluggish, and healing. Here’s how to approach carbs during this fragile but critical rebuilding window:

✅ Stick to the easiest-to-digest carbs:

• Liquid carbs: fruit juice, coconut water, organic lemonade, Italian soda (cane sugar), kombucha (if tolerated), honey, maple syrup, and skim milk (raw is best)

• Whole fruits that have low fiber and seeds: mango, melons, stone fruit like peach and plum

• Cooked, peeled tubers like sweet potato or white potato (only if well tolerated)

⚠️ Fiber carbs must be well tolerated. Avoid if they cause symptoms:

• Sourdough (even well-fermented)

• White rice (especially for those with methane archaea or IMO)

• Berries with seeds

• Potato skins

• Sprouted oats

• Raw salads

• Cassava

• Any raw or undercooked fibrous vegetables

Your gut may handle these better after 2–4 weeks of consistent refeeding with easier carbs.

💡 Important: Everyone digests carbs differently.

Your ability to digest carbohydrates depends on your bacterial diversity, enzyme output, and even stress levels. What works for one person (white rice, sourdough, beans) may not work for another. I always recommend starting with the simplest carbs and slowly layering in fiber once symptoms stabilize and metabolic markers (like body temp and motility) improve.

🧠 The Mental Trap: Blaming Carbs

Most of us have internalized decades of carb-phobia. So when digestion goes haywire, it’s easy to fall back on the belief that carbs are to blame. But let me say this bluntly:

It’s not the carbs. It’s the malnourishment.

Carbs didn’t cause your weight gain. Swampland did (that high-fat/high-carb no man’s land where nothing burns efficiently).

Carbs aren’t triggering your yeast. They’re triggering your immune system to respond as your gut terrain shifts.

If anything, the cut—especially one done with moderate to high fat—is what destabilized your microbiome in the first place.

🔄 The Refeed Feels Worse Than the Cut (And That’s Normal)

Most people expect to feel better when refeeding. More food = better, right?

Not always.

Early refeed can be even harder than the cut itself, because your body is still downregulated:

• Metabolism is low (T3 takes time to rebound)

• Digestion is weak (enzymes are sluggish)

• Detox pathways are backed up (no bile, poor methylation)

• Gut bugs are fighting for dominance

You’re still technically in a malnourished state. But now you’re introducing fermentable fuel. This combo can trigger temporary chaos.

The key? Push through—gently. Don’t overdo fiber. Don’t crank fat back up. Stick to simple carbs and digestible foods. Trust the process. You’re rebuilding.

🧯 My Pro-Metabolic Refeed Rules for Gut Repair:

1. Keep fat ultra-low during early refeed (0.3–0.4 g/kg)

2. Use simple, low-residue carbs (fruit juice, maple syrup, coconut water, Italian soda)

3. Split carbs across 4–5 meals/day for blood sugar and motility

4. Support detox with daily raw carrot or bamboo shoots

5. Temporarily avoid high-fiber carbs unless well tolerated (sourdough, berries with seeds, sprouted grains, etc.)

6. Gradually layer in cooked, peeled tubers only if tolerated

7. Track symptoms and metabolic markers (temps, pulses, stools)

8. Don’t fear a little bloat or gas—it’s part of the rebuild

💥 Summary:

• Gut issues after a cut aren’t because of carbs—they’re because of the cut.

• Carbs feed beneficial bacteria that repair the gut lining and outcompete pathogens.

• The refeed can trigger die-off, not overgrowth—don’t confuse the two.

• Your digestion is compromised post-cut, even for foods you normally tolerate.

• Stay low-fat, stick to easy carbs, and allow time to heal.

• And most importantly: your gut needs nourishment, not another restriction cycle.