Your Gut Has a Circadian Rhythm Too

And this time of year, it’s probably feeling a little confused.

This season always sneaks up on us.

The light fades earlier, dinners shift to dark hours, and before we know it, our whole rhythm starts to drift. It’s fairly subtle right now. Just enough missing light in the evenings to make you feel a little nostalgic for summer. Those sunlit mornings, the warmth of the air, the long walks…they’re slowly disappearing.

Fall is actually my favorite season. I love the smell in the air, the rush you get from enjoying that first cup of warm chai, and the cozy pull of an oversized sweatshirt. But what I don’t love is what’s coming next: the clocks rolling back, the even earlier darkness, and everything that comes with it.

We feel it in our mood and energy first… that midafternoon dip hits harder, mornings take longer to warm up.

But your gut feels it too.

Here’s the fascinating part.

It turns out your digestive system runs on its own clock. And that clock is set by light. Every cell in your gut, from the enzymes in your stomach to the microbes in your microbiome, follows a circadian rhythm. During the day, your body is wired for digestion, absorption, and movement. At night, it’s meant for repair, regeneration, and detoxification.

But when daylight hours get shorter and our routines start to slide, that rhythm gets blurry.

We eat dinner while answering a few more emails.

We stay up scrolling under the soft blue glow of a screen because it feels like the only quiet time we get.

We skip breakfast because the morning is dark and rushed, and just grabbing a coffee feels easier. Little things… but they all send mixed signals. Instead of clear cues of day and night, your body gets constant static:

“Should I digest or rest? Burn or repair?”

And that confusion shows up in small but noticeable ways:

• Feeling bloated or heavy in the morning.

• Waking up less hungry.

• Sleeping lightly or waking around 2–3 a.m.

• Feeling “wired and tired” in the evening.

When your gut’s rhythm is out of sync, so is the timing of everything else. Stomach acid and enzyme production slow down, leaving food sitting heavier. The migrating motor complex (what I like to think of as a street sweeper, which sweeps the stomach and intestines every few hours) can’t run on schedule.

Your gut microbes lose their sense of time, which throws off everything from digestion to mood to hormone signaling.

And because your gut communicates with the rest of your body through hormones like leptin, insulin, and cortisol, this ripple reaches far beyond digestion. It can make energy unpredictable, hunger cues confusing, and sleep full of tossing and turning.

But the fix isn’t complicated. It, of course, comes back to rhythm.

Try treating your gut like a system that thrives on predictability:

Here are a few things you can do:

1. Step outside early.
Natural light first thing in the morning (in your bare eyes) resets your gut’s internal clock, syncing digestion and metabolism for the day. Even cloudy light counts.

2. Eat breakfast earlier.
Even something small with protein tells your body, “It’s daytime.” It stabilizes blood sugar and kickstarts your digestive rhythm.

3. Keep meal times consistent.
Your gut loves routine. Eating around the same times each day helps your enzymes, hormones, and microbes perform efficiently.

4. Give your gut a “night shift”.
What I mean by this is that the goal is to try finishing dinner two to three hours before bed and dimming the lights as you wind down. Darkness is the cue your gut needs to switch from digestion to repair.

5. Don’t aim for perfect. Just aim for steady.
Rhythm isn’t about rigidity; it’s about repetition. The smallest cues… the light, the meal timing, the quiet… are what keep your body grounded through shorter days.

Because here’s the thing:

Fall doesn’t have to mean fatigue, cravings, or restless nights.
When your gut knows what time it is, energy feels steadier, mood lifts, and your system runs smoother.