How Digestion Actually Works

How Digestion Really Works

Most people think digestion happens in the stomach.

It doesn't.

Digestion is a multi-stage enzymatic process that begins in the mouth and ends in the colon — and every stage depends on the one before it.

When one stage fails, everything downstream suffers.

Stage 1 — The Mouth: Where digestion begins

Digestion starts the moment food enters the mouth.

Saliva contains amylase, an enzyme that begins breaking down starches into sugars before you even swallow. Chewing isn't just mechanical — it mixes food with enzymes and creates the first chemical digestion step.

This is why food that is well-chewed digests more easily: The enzymes have already begun their work.

Stage 2 — The Fundus: Howell's "Predigestion Window"

When food reaches the upper stomach (the fundus), something important happens.

Before stomach acid floods in, there is a brief window — roughly 15–20 minutes — where:

  • The pH is still relatively mild
  • Food enzymes from raw or lightly cooked food are still active
  • Supplemental enzymes can still function

Dr. Edward Howell called this the predigestion phase.

During this time, enzymes begin breaking food down before acid shuts them off.

This is not theoretical — you can see it.

When digestive enzymes are added to food, starches and fibers rapidly break down, turning thick, clumpy food into a thinner liquid. This is exactly what happens in the stomach during this predigestion window.

This stage is critical.

If it doesn't happen, the stomach has to do far more work later.

Stage 3 — Acidification: Pepsin is activated

As digestion continues, the stomach releases hydrochloric acid (HCL).

This does three things:

  • It kills microbes
  • It unfolds proteins
  • It converts pepsinogen into pepsin

Pepsin is the primary protein-digesting enzyme of the stomach — but it only becomes active when the pH is low enough.

This is why low stomach acid causes:

  • Poor protein digestion
  • Bloating
  • Reflux
  • Food sitting in the stomach too long

Without enough acid, pepsin never turns on.

What happens to enzymes in stomach acid?

Many people are told that stomach acid "kills" enzymes.

That's only partly true.

Some enzymes denature (are destroyed) in strong acid.

Many fungal and bacterial enzymes deactivate but do not denature — they simply go dormant.

When pH rises again in the small intestine, they become active again.

This is why supplemental enzymes:

  • Help in the stomach during predigestion
  • And continue working later in the intestine

They are not wasted.

Stage 4 — The Small Intestine: Where absorption happens

As food leaves the stomach, it enters the small intestine.

Here the body releases:

  • Pancreatic enzymes (protease, amylase, lipase)
  • Bile from the gallbladder

This is where:

  • Proteins become amino acids
  • Carbohydrates become sugars
  • Fats become fatty acids

Bile emulsifies fats so lipase enzymes can break them down.

Without enough bile or lipase:

  • Fats go rancid
  • Endotoxins form
  • Stools become greasy
  • Inflammation rises

Stage 5 — The Colon: Where what remains must leave

Whatever isn't absorbed moves into the colon.

Here it should be:

  • Mostly water
  • Fiber
  • Mineral residue

When digestion is poor:

  • Proteins rot
  • Carbs ferment
  • Fats become toxic
  • Bacteria explode

This creates:

  • Gas
  • Constipation
  • Inflammation
  • Immune activation

The colon becomes overloaded when digestion upstream fails.

Why enzymes matter

Modern food is:

  • Cooked
  • Processed
  • Refined
  • Enzyme-depleted

Your body is expected to supply all digestive enzymes — but enzyme production declines with:

  • Age
  • Stress
  • Illness
  • Overeating

When enzymes are missing, food becomes a toxic burden instead of nutrition.

Supplemental enzymes restore