Toxins in Coffee: 7 Sources of Harmful Chemicals in Your Morning Brew (Updated 2024)

Coffee is a superfood, and you should feel good about drinking it every day. Organically grown coffee beans are now widely available–this is great! Unfortunately, even organic beans are almost always roasted, packaged, and brewed in ways that can add all sorts of unwanted chemistry to your morning brew.

This means that by the time your organic coffee reaches your cup it would likely no longer qualify as “organic,” and definitely not as Good Stuff.

Gimme’s Own Clean Caffeine

Clean Caffeine is our own line of coffee, made from 100% organic beans that are stored in plastic-free stainless steel and delivered to you in certified non-toxic and 100% compostable bags. This means that our coffee is not only non-toxic (including being free of PFAS) but also a zero waste product. And, it has received only 5-star reviews from our customers.

More recently, we launched a line of 100% backyard-compostable, certified non-toxic K-cup pods for all of our readers with K-cup brewing systems.

ShOP Clean Caffeine

TLDR: You can now buy truly healthful coffee from us. But let’s still look at the seven ways that your coffee can become contaminated, and how to address each one.

Problem #1: Toxins in Coffee Growing

Coffee is one of the most intensively sprayed crops in the world. This is because coffee is no longer grown in the shade (where the plant evolved and thrives). It is now grown in ways that allow for maximum production, but that requires the use of large amounts of pesticides, herbicides, fungicides, and chemical fertilizers.

This is not only bad for us as consumers, but is also devastating to the people who live and work in coffee-producing areas.

Here are just three of the pesticides commonly used on coffee beans:

1. Methyl Parathyion is one of the most vile pesticides ever created, and is toxic to a wide swath of all living things–including humans.
2. Endosulfan is toxic to most animals and takes a very long time to break down in the soil.
3. Chlorpyrifos has been banned for household use in the U.S. as it can cause birth defects.

All of the above, and more, can show up as toxins in your coffee cup every more.

The solution to this problem is pretty simple: Buy only certified organic coffee beans.

Problem #2: Toxins in Coffee Roasting

Organic beans are a great start to a healthier cup of coffee, but it is important that the roasting process be free from harmful chemistry, too.

Some roasting equipment needs to be cleaned on a regular basis to avoid chemical solvents showing up in your cup. Flavoring agents are commonly used immediately after the roasting process, sometimes to mask the taste and smell of old or bad beans. Flavored coffee should be avoided as they often contain preservatives that are definitely not Good Stuff.

Ideally, your coffee beans will be stored in stainless steel rather than plastic drums, where they can pick up microplastics.

The solution here is a little more complicated: Find a roaster that is dedicated to a non-toxic process. (This is easier said than done—it took us a year to find one!).

Problem #3: Toxins in Coffee Bags & Packaging

Once the coffee beans are roasted, they go into a bag. These bags almost always contain plastics and other chemicals that can leach intoyour beans.

Coffee bags typically have a lining of polypropylene to keep the coffee oils from making the bag unsightly. Simple brown paper bags may fool you by looking like they are made entirely of paper, but this is never the case.

Polypropylene, while relatively inert, is the single most abundant micro-plastic found in all the waters of the world (and in seafood…and in every one of us!). The effects of micro-plastics from this type of plastic are only beginning to be understood. Studies have found that polypropylene particles may stimulate the immune system, but human studies are lacking.

Some coffee beans come in glassine bags (like the ones pictured above). This seems better than plastic because glassine is essentially wood pulp. Unfortunately, glassine is almost always bleached with chlorine or other chemicals that stay in the paper fibers and are leached into the coffee beans.

Per- and polyfluoroalkyl substances (PFAS) are another big concern in coffee packaging. Known as “forever chemicals,” these are often used in food packaging because of their water- and grease-resistant properties, but they can leach into the food or drink they come into contact with. In the case of coffee, PFAS-lined bags help preserve freshness by creating a barrier against moisture and oils. Once these chemicals enter the body, they don’t break down easily and can accumulate over time, potentially leading to serious health issues such as hormone disruption, immune suppression, and cancer. Finding a bag without a PFAS lining was the single hardest part of developing our own line of coffee.

We’ve solved this one for you! Until recently, there have been no alternatives to standard coffee bags, but we finally found a new, non-toxic, environmentally safe alternative that’s free of PFAS.

The Worst Stuff: Coffee Pods

Even worse than the bags used to store coffee beans or ground coffee are coffee pods. The environmental damage caused by coffee pods (AKA “K-cups”) can’t be overstated. In fact, their founder, John Sylvan, has said that he regrets inventing the pod!

Traditional coffee pods are neither biodegradable nor recyclable, and a whopping THIRD of American households have a K-cup brewer in their homes.

Equally concerning: coffee pods are made of plastic, and the hot water that passes through them increases the leaching of endocrine disruptors into your coffee. While K-cups are free of BPA, they’ve still tested positive for estrogenic activity.

To make matters worse, the top of coffee pods are usually made of aluminum, a heavy metal linked with a range of health problems.

There are quite a few versions of K-cups that advertise themselves as being compostable, but this typically means that they will break down within the context of “commercial composting.” In other words, it will take a very long time for those products to decompose into soil unless your municipality has a very specific type of commercial composting facility. Most of these plastics will also not biodegrade in a landfill.

Fortunately, we’ve solved this problem with our truly compostable, PFAS-free K-cups.

Problem #4: Toxins in Coffee Water

Obviously, brewing coffee starts with water. If you use typical municipal water you are adding chlorine, fluoride, and potentially substances like lead, pharmaceuticals, PFAS, pesticides, and others to you morning cup. Not only are these toxic, but they can also negatively affect the taste of your coffee.

The solution here is easy: We highly recommend using a robust water filtration system. Pitcher type filters are better than nothing, but true filtration essentially eliminates a very wide swath of biological agents and chemical toxins. Learn more about choosing a water filter here.

Problem #5: Toxins in Coffee Brewing Equipment

Water is a potent solvent that breaks down many substances. Hot water is an especially intense solvent, and it extracts substances far faster than cold water does.

Whether you like cold-brew or hot, pour-over, drip, espresso, French press, or a plug-in brewer, it is a good idea to avoid brewing equipment that is composed of certain plastics, metals, or coatings that could introduce unwanted substances into your cup.

More specifically, you’ll want to avoid coffee brewers with plastic parts that come into contact with water. Also, avoid aluminum, non-stick surfaces, and any low-fire ceramics.

The good news is that there are several great ways to brew without any toxins. We like stainless steel filtration rather than plastic, paper, or even cloth. Stainless steel is rugged, easy to clean, imparts no flavor, and lasts almost forever—making it an Earth- and wallet-friendly choice.

As for coffee dispensers, cups, and storage, we like stainless steel, glass, and most ceramics. Medical grade silicone seals are acceptable and better than plastics.

The solution here is to vet your coffee accessories carefully. We really like this brand.

Problem #6: Toxins in Your Coffee Cup

You may already know that styrofoam cups can mess with your hormones, especially when the liquid inside of them is hot! But even paper to-go coffee cups can be a problem, from the coating on the inside (polyethylene) to the glue at the seams–which partially dissolves when the coffee is poured into the cup. Moreover, wax-coated paper cups cannot be recycled because of their petroleum-derived paraffin coating.

Coffee lids made with #6 or #7 plastic likely contain BPA. The last few times I’ve ordered a to-go coffee I’ve noticed the lid is printed with a #7, and of course you’ve got hot liquid passing through this on it’s way to your mouth (like in the picture of Maia above!).

The solution here is to bring your own reusable coffee mug when stopping at a Starbucks. I like this one.

Problem #7: Toxins in Decaf Coffee

If you are a drinker of decaf coffee, you have one more thing to worry about. There are two primary decaffeination techniques, only one of which is Good Stuff.

1) Methylene Chloride Process (MCP)
Also known as “direct decaffeination,” MCP is the most common decaffeination technique. MCP decaffeination uses the solvent methylene chloride (commonly found in things like paint stripper), and it leaves behind trace amounts of this toxin. According to Consumer Reports, higher doses of methylene chloride “can cause headache, confusion, nausea, vomiting, dizziness, and fatigue, and has been found to cause liver and lung cancer in animals.” It’s true that the amount of methyl chloride that remains in decaf coffee is restricted to not exceed 10 ppm, but I definitely want my coffee free of this decidedly Bad Stuff.

2) Swiss Water Process (SWP)
In this method, coffee beans are soaked in near-boiling water, which extracts both the flavor oils and the caffeine from the coffee. The water is then separated into a tank, where it is forced through charcoal filters to remove the caffeine. The beans are then reintroduced to the swill, which reabsorbs the flavor. Since no chemicals are used, there’s nothing to worry about in terms of toxins with SWP decaf coffee.

The bottom line if you drink decaf coffee: Make sure it’s water-processed! (Ours is, of course!)

What About Mycotoxins in Coffee?

Mycotoxins are toxic compounds produced by molds that can grow on certain foods, including coffee, when stored in humid or improperly dried conditions. These toxins are commonly associated with foods like grains, nuts, dried fruits, and spices, which, like coffee beans, are susceptible to mold contamination if their moisture levels are too high.

The good news is that if you’re choosing high-quality coffee, mycotoxins are almost certainly not present. Coffee beans with a moisture content below 14% and a water activity level under 0.65 are unlikely likely to harbor mycotoxins, making careful drying and storage essential for quality and safety. (Our coffee moisture content is around 9.5% and a water activity level of 0.4.) Testing for mycotoxins in coffee is not always useful, because mycotoxins are often unevenly distributed in coffee beans, meaning a sample from one part of a batch may not represent the entire batch. This “hotspot” distribution makes it hard to obtain a truly representative sample, and a batch could pass or fail testing depending on where the sample was taken.

Opting for organic, single-origin beans from reputable sources with transparent practices is the best way to protect yourself against mycotoxins from your coffee.

Why We Think Clean Caffeine Is the Best Stuff

Our coffee is made of certified organic coffee beans that are fresh roasted. Each bag has a roast date. Our beans our stored in special stainless steel containers–they never touch plastic during the roasting process!

Our packaging is certified non-toxic by an independent testing facility. This means that the bags, the valve, the labels, the ink, and even the adhesives are nontoxic and 100% compostable. The packaging is free of BPA, phthalates, PFAS, fossil fuel by-products, and bleach.

We now offer Swiss processed decaf as well. And, our coffee moisture content is around 9.5% and a water activity level of 0.4. As mentioned above, mycotoxins are produced when a product has a moisture content over 14% and a water activity level above 0.65.

Importantly, our Clean Caffeine has gotten only 5-star reviews from our customers, and most people who order a bag decide to subscribe to keep it coming uninterrupted.

Coffee Alternatives We Love

What if coffee is something that you love but it doesn’t love you back? Coffee is delicious and I love the ritual of it after breakfast, in the afternoon, or after dinner. But caffeine makes some people, my wife included, agitated and impatient, and it can disrupt sleep or cause indigestion. Even decaf can sometimes bother some people’s stomachs. Suzanne recently discovered MUD/WTR, and it’s taken the place of her morning latte. It is full of superfoods, and is soothing, warming, and gives a little lift without any of the side effects that she experiences with coffee. Two other superfood coffee alternatives to try: Pique’s Nadanka and Roots Apothecary Mushroom Cacao.

If getting caffeine from tea is more your speed, look no further than our post on how to avoid toxins in tea.

Stay sane,

John, Certified Holistic Health Coach

Shop This Story