The Hidden Toxins in Your Daily Coffee – What You Need to Know

Coffee has always been a bit of a ritual for me. I loved everything about it, the smell, the warmth, the pause it gave me in the middle of a busy day. Back before my functional health journey began, I was a loyal Costa Coffee fan. I’d sometimes opt for a decaf if I was feeling a bit jittery (I’m the sort of person who can get the shakes from too much caffeine), but I never thought twice about the coffee itself. It was just part of life.

That was until I started working with a functional medicine practitioner. Over the past year, I’ve been uncovering how many everyday products we consume, without a second thought, can contain hidden toxins. Coffee, to my surprise, was one of them. It wasn’t about giving it up forever, but it became clear that, for now, cutting it out would reduce some of the unnecessary toxins going into my system. These days, I’ve swapped it for an organic chicory root drink, which surprisingly hits the spot.

Looking back, it all makes more sense. I remember the odd time I’d grab a McDonald’s coffee and feel nauseous halfway through, or the unwell, unsettled feeling that sometimes followed a takeaway brew. At the time, I brushed it off. But now, knowing what I do about the way coffee is processed and the toxins it can carry, I can’t help but wonder, was it the caffeine… or was it something else entirely?

In this article, we’re diving deep into what’s really in your coffee, especially those from supermarket shelves and high street cafés. We’ll explore the toxins that may be hiding in your cup, how coffee (and decaf) is processed, and what you can do to make cleaner, healthier choices without giving up your favourite morning ritual.

From Bean to Brew – The Coffee Journey

Before coffee lands in your mug, it’s already gone through a long, complex journey, one that most of us never really think about. But understanding how coffee is grown, harvested, processed, and roasted gives us important insight into where toxins can quietly creep in.

Let’s start at the source: the humble coffee bean.

Coffee is typically grown in developing countries along the equator, where warm, humid climates create the perfect environment for growth but also for pests, mould, and fungi. This means many large-scale farms rely heavily on chemical pesticides, fungicides, and synthetic fertilisers to protect the crops and maximise yield. Unfortunately, these chemicals don’t just disappear before the beans reach us. Unless coffee is grown organically, there’s a good chance it contains residues of these substances.

After harvesting, the beans go through a series of steps: they’re washed, fermented, dried, and stored, often in bulk warehouses where humidity and airflow can be inconsistent. If these steps aren’t done carefully (which is common in large-scale operations), mould can form on the beans. That’s when mycotoxins, naturally occurring but harmful compounds like ochratoxin A, can develop. Some of these are known to affect kidney function, brain health, and immunity.

Then comes roasting. While roasting is what gives coffee its delicious, rich flavour, it also creates something less appetising: acrylamide. This chemical forms when foods are cooked at high temperatures and is considered a potential carcinogen. The darker the roast, the more acrylamide may be present, although even light roasts aren't off the hook.

Finally, there’s packaging. Some low-quality brands use bags or pods lined with plastic, glues, or coatings that can leach chemicals, especially when exposed to heat or moisture. Yet again, it’s another hidden layer most of us never considered.

So by the time your coffee hits the supermarket shelf or is poured into your paper takeaway cup, it’s travelled through pesticides, mould risks, high-heat roasting, and packaging that may not be as “safe” as we assume. That’s a lot for one innocent-looking brew and it starts to explain why some coffees just don’t sit right.

Decaf vs Regular – What’s the Real Difference?

For a long time, I thought decaf coffee was the “healthier” option. After all, if caffeine makes you feel jittery or gives you a crash, cutting it out feels like the sensible thing to do, right? I’ve always been someone who can be sensitive to caffeine, too much and I’d get the shakes, a racing heart, or even feel nauseous. So occasionally, I’d opt for decaf thinking it was a gentler alternative. But what I didn’t know back then was that decaf coffee can come with its own set of problems, especially when it comes to how it’s made.

Let’s start with the basics. To remove caffeine from coffee beans, companies use one of several methods. The most common (and cheapest) involves chemical solvents, often methylene chloride or ethyl acetate. Methylene chloride, in particular, is concerning, it’s used in paint strippers and has been linked to potential liver and lung toxicity. The beans are soaked in these solvents to strip out the caffeine, and while companies claim the residues are “minimal,” they’re rarely tested or disclosed. If you’re drinking decaf from a generic supermarket brand or café, this is often the method used.

But there’s good news too. There are cleaner, chemical-free ways to decaffeinate coffee, the most well-known being the Swiss Water Process. This method uses water, temperature, and time to gently remove caffeine without adding any nasty chemicals. It also preserves more of the coffee’s natural antioxidants. Another clean option is the CO₂ (carbon dioxide) method, which uses pressurised CO₂ to pull caffeine out of the beans, safe and effective, but more expensive, so not as widely used.

The big issue is that most coffee brands don’t tell you which method they use unless it’s a selling point. That means unless you see “Swiss Water Process” or “CO₂ decaffeinated” clearly labelled, you can almost assume it’s the cheaper chemical route.

And here’s something that surprised me: decaf beans are often lower quality to begin with. Since many people view decaf as a second choice, some companies don’t put the same care into sourcing or testing the beans they use, making them even more prone to mould and toxins.

So while decaf may feel like a safer option for those sensitive to caffeine (like me), the way it’s processed really matters. Without that awareness, we might be trading one issue, caffeine, for another that’s hidden and potentially more harmful.

What Toxins Are Found in Coffee?

We don’t usually think of coffee as something that could contain toxins. In fact, it's often promoted as a health drink, packed with antioxidants, supporting brain function, even protecting against disease. And while there’s truth to that when it’s clean, high-quality coffee, most of what’s found in supermarkets and high-street cafés is far from pure.

Here are some of the most common toxins that can sneak into your daily brew:

1. Pesticides and Herbicides

Unless your coffee is certified organic, the beans were likely treated with a cocktail of synthetic pesticides and herbicides. These chemicals help farmers boost yields and keep pests away, but they don’t just vanish before the coffee reaches you. Long-term exposure to these residues, especially in daily habits like coffee, has been linked to hormone disruption, gut imbalances, and even certain cancers.

2. Mycotoxins (from mould)

Coffee is a high-risk crop for mould contamination. During harvesting, drying, and storage, especially in humid regions, beans can easily develop mould. This is where mycotoxins, like ochratoxin A, come in. These compounds are invisible, heat-resistant, and have been linked to kidney damage, immune suppression, and neurotoxicity. If you’ve ever felt weirdly foggy, sick, or anxious after coffee, this could be why.

3. Acrylamide

This chemical forms when coffee beans are roasted at high temperatures. It’s a by-product of the Maillard reaction (the same process that browns toast), and unfortunately, it’s classified as a potential carcinogen. While small amounts are present in many roasted foods, regular exposure through a daily coffee habit adds up.

4. Solvent Residues (in decaf)

As mentioned earlier, many decaf coffees use methylene chloride or ethyl acetate to remove caffeine. Even though these are said to be “rinsed off,” trace amounts can remain. Methylene chloride has been linked to nervous system effects and even cancer in some animal studies. And if the beans weren’t high-quality to start with, you’re essentially soaking already-questionable beans in chemicals before drinking them.

Why Most Supermarket and Café Coffees Aren’t Clean

We tend to assume that the bigger the brand, the safer the product but when it comes to coffee, that couldn’t be further from the truth.

Most of the coffee sold in supermarkets or served in high-street cafés like Costa, Starbucks, and McDonald’s is mass-produced on a huge scale. To keep prices down and supply consistent, these companies often use low-grade beans sourced in bulk from industrial farms. And here’s where the problem starts.

Cheap beans usually come from farms that rely heavily on chemical farming methods, using pesticides and herbicides that aren't removed before roasting. The beans are then processed quickly, stored for long periods, and often roasted in massive batches without proper testing for mould or mycotoxins. There’s very little incentive for these companies to prioritise toxin screening because most consumers have no idea it’s even an issue.

Even more concerning is the lack of transparency. Most big-name coffee brands don’t tell you how their decaf is processed, where the beans were grown, or whether they’ve been tested for mould. And if they don’t say they use the Swiss Water or CO₂ method? You can assume it’s the cheaper chemical route.

Looking back, this explained a lot for me personally. I remember drinking a coffee from McDonald’s once, something I only did on rare occasions and about halfway through I’d suddenly feel sick and unsettled. At the time, I thought maybe I hadn’t eaten enough, or maybe it was just “strong coffee.” But now, knowing what I do about the lack of regulation and quality control in these big chains, I can’t help but wonder if it was more than just caffeine hitting my empty stomach.

It’s not that these companies are trying to harm people, it’s simply that profit and scale take priority over purity. And unfortunately, unless we know what to look for, we’re the ones left sipping on a cup full of invisible extras.

Why We Never Knew This Before

When I first started learning about toxins in coffee, my reaction was probably similar to yours: Why haven’t I heard any of this before? For something so many of us drink daily, often without a second thought, you’d think we’d be more informed. But the truth is, we’ve never really been told to ask the right questions.

Big coffee brands are incredibly good at marketing. They highlight things like roast strength, origin, or fancy-sounding flavour notes, caramel swirl, chocolate finish, hints of hazelnut, but they rarely talk about how the beans were grown, processed, or tested. It’s a carefully crafted image that keeps us focused on taste and convenience, not safety.

On top of that, coffee is often painted as a health hero. Articles and influencers share all the benefits, boosted metabolism, antioxidants, brain support and while those benefits can be true for clean coffee, they’re usually shared without any mention of the risks tied to poor-quality brews. There’s little talk of mould toxins, solvent residues, or pesticide load because it doesn’t sell well. And unless you’re already diving into the world of functional medicine or holistic health, you probably won’t stumble across this information.

There’s also the trust factor. We tend to assume that if something’s being sold in a supermarket or by a major chain, it’s been properly tested and approved. But in reality, there’s no requirement for coffee brands to test for moulds or toxins, and hardly any oversight into how decaf is processed. Clean, toxin-free coffee is still very much a niche market.

I only began questioning it all once I started working with a functional medical practitioner. It was part of a bigger conversation around reducing my toxic load and supporting my body’s healing. And once I started looking into coffee more closely, I was shocked at how much I didn’t know, and how easy it was to believe that all coffee was more or less the same.

But now I know better, and I want others to know too, because small changes, like switching your coffee, really can make a big difference over time.

What to Look for in a Clean Coffee

Once you know what might be lurking in your daily cup, the next step is making some conscious swaps, not from a place of fear, but from a place of empowerment. You don’t have to give up coffee completely (unless you're on a healing plan like I am); you just need to make more informed choices.

Here’s what to look for when choosing a healthier, cleaner coffee:

1. Organic Certification

This is your first layer of protection. Organic coffee is grown without the use of synthetic pesticides and herbicides, which means you’re already avoiding a major source of chemical exposure. Look for certified organic logos, such as USDA Organic or Soil Association Organic (UK), on the packaging.

2. Mycotoxin and Mould Testing

This one isn’t always advertised, but some coffee brands go the extra mile to test their beans for mycotoxins, including ochratoxin A. These are the types of companies you want to support. If it’s not stated on the packaging, check the company’s website or send them a quick message. The transparent ones are usually proud to share this info.

3. Swiss Water or CO₂ Process (for decaf)

If you drink decaf, this is non-negotiable. Avoid anything that doesn’t clearly state it uses the Swiss Water Process or CO₂ extraction. These methods don’t use chemical solvents and are much safer for regular consumption. If it just says “naturally decaffeinated” without more detail, dig deeper.

4. Single-Origin or Small-Batch Roasting

Coffee that’s single-origin (sourced from one location) or roasted in small batches is often higher quality and handled with more care. These coffees are less likely to be bulk-blended with poor-quality beans or mass-stored in mould-prone conditions.

5. Grown at High Altitudes

Coffee grown at high elevations tends to develop less mould, thanks to cooler temperatures and slower growth. If a coffee brand mentions “high-altitude grown,” it’s a promising sign.

6. Transparent Sourcing

The best coffee brands are proud of their sourcing methods and will clearly explain how their beans are grown, processed, roasted, and tested. If a company is vague or uses lots of buzzwords with no substance, it’s probably not your best bet.

Once I made the switch, I noticed a huge difference, not just in how I felt physically after drinking it, but also in peace of mind. I knew I wasn’t unknowingly exposing myself to toxins every morning, and that’s a powerful feeling.

Clean coffee might not be the cheapest on the shelf, but when it comes to something we drink every single day, I genuinely believe it’s worth it.

What You Can Do About It

Now that you know what might be hiding in your daily cup, the next step is making some conscious swaps,not from a place of fear, but from a place of empowerment. You don’t have to give up coffee completely (unless you're on a healing plan like I am); you just need to make more informed choices.

Here’s what you can do to reduce your exposure to coffee-related toxins:

1. Switch to Organic, Toxin-Tested Coffee

Start by upgrading your beans. Choose organic, single-origin coffee from a company that tests for mould and mycotoxins. Some of the cleanest brands are incredibly transparent, listing test results or certifications on their websites. If it’s not obvious, ask, they’ll either proudly tell you or… not reply, which says a lot too.

2. Choose Decaf Carefully

If you prefer or need to avoid caffeine, make sure your decaf coffee uses the Swiss Water Process or CO₂ method. Avoid anything that mentions chemical solvents or doesn’t say how it’s decaffeinated at all. No label often means bad news.

3. Try Natural Alternatives

If you’re cutting coffee out completely for a while (like I am), don’t worry, you still have options. I now drink an organic chicory root drink, which has a rich, coffee-like taste without any caffeine or toxins. Other options include roasted dandelion root, carob, or even adaptogenic blends with reishi or ashwagandha.

4. Brew Smarter at Home

Avoid plastic pods or low-quality paper filters that may contain bleach or glue. Instead, use a stainless steel French press, ceramic pour-over, or glass coffee maker. Clean, non-toxic equipment matters too.

5. Store Your Coffee Properly

Once you’ve found a clean brand, make sure you store it well. Keep it in an airtight container in a cool, dark place. Mould can still grow in beans that are exposed to heat and moisture, even at home.

6. Tune Into How You Feel

This might sound simple, but it’s powerful. After you drink your coffee, pay attention. Do you feel steady and energised or shaky, foggy, or slightly sick? Your body often knows before your brain does. Don’t ignore those signals.

The beautiful thing is, once you know what to look for, you’re in control. Whether you’re ready to upgrade your daily cup, experiment with alternatives, or pause coffee altogether, you’re taking a step toward supporting your body, not burdening it.

And honestly? That morning ritual feels so much better when it’s aligned with your wellbeing.

Is It Worth Spending More?

Let’s be honest, clean coffee isn’t always the cheapest option. When you start looking at organic beans that are mycotoxin-tested, ethically sourced, and decaffeinated using safer methods, the price tag can go up. And if you’re used to grabbing a jar of instant or a drive-thru brew, it might feel like a big jump.

But here’s the thing: you’re already investing in your health every day, whether you realise it or not. The question is, are you investing in what supports your body, or in what slowly depletes it?

Coffee is something many of us drink every single day. That means it has the potential to either nourish you… or quietly chip away at your health. When you zoom out and consider what you might be avoiding, chemical exposure, long-term toxin buildup, unexplained symptoms like anxiety or nausea, it starts to feel like a very worthwhile trade-off.

And it doesn’t always mean spending a fortune. Some clean brands offer subscription discounts or smaller bags to try before committing. Plus, when you invest in quality, you often need less to feel satisfied. A single clean, well-roasted cup can give you a better lift than multiple mugs of low-quality coffee ever could.

For me, once I learned what was really in most conventional coffees, the price of a cleaner option felt like a small price to pay for peace of mind. And once I removed coffee entirely, at least for now, I actually saved money without feeling like I was missing out, thanks to a comforting and affordable chicory drink.

At the end of the day, it’s about making informed choices that align with your values and your health. If something feels off in your body after drinking coffee, that’s information. If switching brands makes you feel better, that’s confirmation. And if paying a little more means you avoid hidden chemicals or toxins, then ye, it’s worth every penny.

Final Thoughts – Rewriting Your Coffee Ritual

If there’s one thing I’ve learned on this journey, it’s that knowledge really is power, especially when it comes to the small, everyday habits we don’t question. Coffee was once something I reached for without thinking. It was part of my morning, part of my comfort, and part of how I connected with people. But now, I see it differently.

When I began working with a functional medicine practitioner and started learning about the toxic load our bodies carry, often without us realising, coffee was one of the first things I chose to let go of. Not forever, just for now. And not because I no longer love it, but because I finally understood what might be hiding in it.

That occasional sick feeling halfway through a café coffee. The shaky hands after a decaf. The slight nausea that I once brushed off. They all started to make sense.

The beauty is, you don’t have to give up coffee entirely to make a change. You just need to get curious. Ask questions. Check labels. Try new things. Whether that means switching to an organic, mould-free brew, choosing Swiss Water Process decaf, or taking a break with a nourishing alternative like chicory root, it’s about being in alignment with your health rather than working against it.

We often think we have to accept the way we feel after coffee. But what if you didn’t have to? What if the right cup actually supported your energy, your gut, your nervous system, without leaving you depleted?

I truly believe that with the right choices, your daily coffee ritual can still be sacred, just cleaner, gentler, and more supportive for your body and mind.

So here’s to rewriting the ritual, consciously, confidently, and with a little more care in every cup.