Is Coffee Harmful To Your Health?

That morning cup might feel like a trusted friend — but is it quietly working against you? Coffee’s reputation has swung from health hero to hidden hazard and back again. The truth is far less black-and-white… and far more interesting. Let’s cut through the noise and look at what coffee really does to your body, so you can decide how it fits into your health.

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Table of Contents

The Truth About Coffee
Scientific Data Around Coffee
Coffee & Your Genetics
How Do You Feel About A ‘Caffeine Holiday’?
Coffee & Body Weight
Coffee & Energy Levels
When Should You Have Coffee?
Important Considerations for Coffee
The First Step is Awareness

The Truth About Coffee

Let me cut right to the chase, the short answer on coffee is that if you enjoy some coffee and don’t have any real issue in terms of anxiety or sleep or food cravings, it’s likely harmless — there may even be some slight benefit in drinking it.

On the other hand, if you have sleep problems, abnormal cortisol, anxiety, or blood pressure issues, your coffee could be part of the problem. Even just a cup per day. Even if you’ve had it for years.

Now that we have that out of the way, let’s dive a bit deeper…

Scientific Data Around Coffee

Prior to the early 2000s, some notable studies found that coffee intake had a strong correlation with cardiovascular death (heart attacks, to be specific). This was true even in small amounts and led to the idea that coffee was more of a vice than a virtue.

Here’s the thing: It turned out that these studies were all of a certain type. They were all older and looked specifically at Nordic populations who were consuming unfiltered coffee. This is kind of like “cowboy coffee,” which involves only a very loose straining of the coffee grounds.

The thing with that is that, when you have loads of these compounds that are unfiltered, they can be incredibly harmful to your cardiovascular system. When we keep that in mind, it becomes pretty obvious how coffee began to get painted in this light.

But in modern usage, with filtered coffee, that is very different. Another group of more modern studies found that higher intakes of coffee had numerous health benefits. This tracks with a typical rule when it comes to plant foods: if it tends to stain, it’s good for you.

This staining is a function of plant pigments, and these are mostly referred to as polyphenols. Many of these polyphenols can act as:

• Antioxidants
• Cofactors in connective tissues

In general, they do a lot of good stuff in the body! When we had studies that suggested the positive health outcomes of coffee, this all began to track quite well.

Now, a lot of these studies turned out to be tied quite closely to socioeconomic status. It seemed that a lot of the benefits were tied more to this status rather than the coffee itself. This kind of ruled out the idea that coffee in higher amounts is the ideal.

Coffee & Your Genetics

One big wrinkle when it comes to the scientific data on coffee is that there is a lot of genetic variation in coffee clearance. This means that coffee has many different constituents, of which one of the big ones is caffeine.

Caffeine is a biologically active alkaloid. When we ingest it, our liver breaks it down into other constituents and eventually eliminates it. How long that takes and how we respond in the interim is highly dependent on our genetics.

There are many people who drink coffee all the time and go to sleep right afterward. And there are others who have the tiniest amounts and can’t catch a wink — you probably know people who fall into either camp, showing how different it can be!

This can also change. There are those who may drink too much coffee and create a sort of intolerance that makes them immune to its effects.

Some studies have looked at cardiovascular outcomes and separated people based on their gene variations. What they’ve found is that those who have the genres commensurate with poor clearance of coffee are the people with higher rates of cardiovascular death.

Ultimately, while we do have gene types and gene expressions, all of the signals you already need are likely right in front of you. When it comes to caffeine, your personal tolerance is likely telling you everything that you need to know.

How Do You Feel About A ‘Caffeine Holiday’?

How does the idea of taking a break from coffee make you feel? If the idea of missing coffee freaks you out, you might be someone that is better off having less of it.

Over the years, I’ve had so many people who have struggled with anxiety or insomnia, or high blood pressure. Before I went deep into diagnosing odd conditions or talking about various exotic treatments, I would simply start by asking them about their caffeine intake.

More specifically, asking them when the last time they had taken a serious break (a couple of weeks or more) from caffeine. And many folks had not taken a break for years — and they couldn’t even imagine a world where they would take a break from it.

The trend that I observed was that the more someone felt freaked out or was opposed to the idea of taking a break from coffee, the more they needed it. And the more likely they were to have a transformative, positive experience from taking that break.

Coffee & Body Weight

There is a stage that we go through called hepatopause, where our liver works differently (this typically goes hand in hand with other ‘pauses’ like menopause). After this phase, our liver may not process caffeine in the same way that it did beforehand.

Somewhere around your mid-forties or fifties, caffeine may work differently for you. In those cases, it may have a more negative effect on body weight.

Coffee & Energy Levels

Caffeine works by blocking adenosine receptors in the body. If we take a step back, we know that our entire body makes energy by using a molecule called adenosine triphosphate (ATP).

When there is a lot of adenosine (without the phosphate) floating around in your body, that’s a signal that it’s time to slow things down and time to become tired. You need to take a rest in order to replenish your ATP.

Especially in the brain, there are receptors for that. Caffeine works by blocking these receptors – but not taking adenosine away – basically blocking your body’s ability to understand that it’s tired. You’re no longer aware that you’re tired, even if you’re definitely tired!

When Should You Have Your Coffee (or Any Caffeine)?
Caffeine is not just in coffee. You will also find it in tea, chocolate, sodas, and some supplements.
No matter the source, your body handles caffeine through the same core pathways.
Timing determines whether it helps or gets in your way.

• Why not first thing in the morning?
  On waking, cortisol is naturally high. Cortisol is your built-in alertness signal.
  Adding caffeine at this time does not multiply alertness.
  It can blunt your natural rhythm and increase reliance on caffeine just to feel normal.
• The mid-morning sweet spot
  Around 9:30–11:00 a.m., cortisol tapers. Caffeine taken in this window provides a clean lift without
  colliding with your hormonal rhythm. Many people also avoid a midday crash by shifting their first cup to this time.
• Adenosine and fatigue signals
  Caffeine blocks adenosine receptors. Adenosine itself continues to accumulate.
  If you use caffeine too early or too often, you mask fatigue rather than resolve it.
  The result can be feeling wired yet unrefreshed.
• Early afternoon is still fine
  Caffeine has a half-life of roughly 6–8 hours. Enjoying a cup in early afternoon can work well.
  After about 2:00 p.m., the risk of impaired sleep increases, even if you can fall asleep.
  Poor sleep then drives the next morning’s craving.
• Applies to more than coffee
  Black and green tea act through the same pathways, even if they feel gentler.
  Chocolate contains smaller amounts that still matter for sensitive people.
  Energy drinks and sodas often pair caffeine with sugar, which adds extra variables.
  The same timing rules apply across sources.

Key Insight: Let your natural cortisol handle the wake-up first.
Use caffeine to extend alertness, not to replace your morning rhythm.
Aim for mid-morning through early afternoon, and avoid late-day intake.

How to Apply This in a Typical Day

1. Wake-up: Hydrate and move a little. Skip caffeine for the first 60–90 minutes.
2. First dose: Have coffee or tea around 9:30–11:00 a.m.
3. Optional top-up: If needed, a small serving in early afternoon.
4. Cut-off: Avoid caffeine after ~2:00 p.m. to protect sleep quality.

Important Considerations for Coffee

If you’re somewhere where you enjoy a cup of coffee most days, take it or leave it, then you don’t really have anything to worry about. There’s nothing you need to necessarily change.

Of course, you should always consider the quality and purity of your coffee. You’ll also want to enjoy filtered coffee to avoid the cardiovascular risks of the unfiltered variety,

There’s also the pH effects, where caffeine can often be acidic and harm your gut. For that reason, you may prefer to have your coffee with a bit of milk.

On the other hand, if you’re someone who doesn’t tolerate it and it makes you feel anxious or jittery, that might already be your sign to avoid coffee. You can skip it and do totally fine.

Some do fine with coffee every now and again, or others do fine with decaffeinated products. It really depends on the person, but these can be options.

Finally, if you’re someone who does enjoy coffee on a regular basis, I would always encourage taking a little caffeine holiday and avoiding it for a few weeks.

This will allow your adenosine receptors the ability to reset, and you can see if your caffeine clearance has changed or any symptoms that snuck up on you without noticing.

The First Step is Awareness

If you feel like you’re doing everything right and still not feeling better, going on a coffee holiday may be one way to find out what’s plaguing you. But what if it has nothing to do with that?

Something like your thyroid health is absolutely critical, and thyroid issues may be the root cause behind why so many other aspects of your health aren’t performing as well.

In fact, the wrong nutrients can keep your thyroid from working its best. If you’re curious about which ones are going to benefit you the most, please consider taking this quiz I put together to help.

I’ll ask you some questions about your health and provide a unique formula based on my Thyroid-Specific Formulations to help optimize your health within your context.

After all, your health journey starts with you. If you want a partner you can trust, I hope you’ll give my quiz a try to see the next steps you can take to really own that adventure. Here’s to your best health!