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How to Make the Healthiest Cup of Coffee

Brian Comly

“We want to do a lot of stuff; we're not in great shape. We didn't get a good night's sleep. We're a little depressed. Coffee solves all these problems in one delightful little cup.”

-Jerry Seinfeld



Coffee used to be an afterthought to me during the day but since having kids it’s one of the first things I think of in the morning. It turns out I’m not alone.

About 66% of Americans drink coffee and 80% of them drink at least one cup at home daily.  Many studies, including this umbrella review of meta-analyses, conclude that coffee has a wide variety of benefits such as lowering all-cause mortality, cardiovascular disease, and cancer risk. There are a lot of theories as to why this is but one of them is that those cups of Joe provide the greatest source of antioxidants in our modern diet.

So just drink more coffee and I’m good? Not so fast. Just because coffee is generally considered to be healthy, doesn’t mean the cup of coffee you’re making in the morning is healthy. In fact, many of us brewing our own coffee may be doing more harm than good by getting a daily dose of toxins with that jolt of energy.  

Let’s dive into the science for how to make the healthiest cup of coffee.

How To Make The Healthiest Cup Of Coffee


The Growing Process And Mycotoxins

Coffee used to grow in the shade but given the world’s love of it there isn’t enough shade for those beans so it’s grown in fields.  This means that it’s one of the most sprayed crops in the world with frequent exposure to herbicides, fungicides, pesticides, and chemical fertilizers.  Additionally, through the processing of coffee, mycotoxins are also found in coffee.  Mycotoxins are toxic compounds created by certain fungi (mold) and found in coffee (among other things).  Here are some common toxins found in coffee.

  • Ochratoxin A (OTA): OTA is a “neurotoxic, immunosuppressive, genotoxic, carcinogenic and teratogenic mycotoxin” (wow).  It creates oxidative stress and disrupts protein synthesis and immune system function.

  • Acrylamide: Acrylamide is a neurotoxin and a probable human carcinogen.  This mycotoxin appears when coffee is roasted but then the heat itself actually kills it so choosing a medium or dark roast is better than a light one for this reason.

  • Aflatoxin B1: Aflatoxin B1 is a carcinogen (linked to liver cancer) produced from mold.

  • PAH (Polycyclic Aromatic Hydrocarbons): PAH is a probable carcinogen that is found in foods cooked at high temperatures (think burnt burgers at a BBQ) or roasted at high temperatures such as in the case of coffee.  

  • Pesticides: Some pesticides found in coffee are methyl parathyion, endosulfan, and chlorpyrifos (banned in the U.S. because it causes birth defects). Pesticides are linked to many health issues such as ADHD and low IQ in kids, cancer, depression, and respiratory issues.

Due to the processing methods of coffee, it’s unlikely that you can completely avoid toxins.  That being said, you can lower your risk of these compounds by choosing high-quality organic coffee which has strict standards of harvesting and roasting coffee with non-GMO crops and low pesticides. 

Do this: 

  • Choose brands that use safe techniques for harvesting and processing their coffee including storing beans in temperature-controlled facilities (to prevent mold growth).

  • Avoid light roast coffees which may not kill some of the toxins.

    Choose coffee roasted in a smokeless machine which reduces toxic compounds and increases the number of antioxidants in the coffee.

  • Once you buy the coffee, store it in a dark, airtight container like this one.

The Roast: Light, Medium, or Dark?

Roasting coffee beans is the part of the process that gives the beans their color, flavor, and aroma.  A light roast is considered 10 minutes or less at 350°F-400°F, a dark roast is 15 minutes at 400°F, and medium is somewhere in between.

Lighter roasts are shown to contain more antioxidants which decrease as the roasting increases to dark. A lighter roast, however, means less time to kill the neurotoxin acrylamide.  The presence of acrylamide is highest in light roast and lowest in dark roast from multiple sources.  So light roasts mean more antioxidants and more toxins but dark roasts mean fewer antioxidants but fewer toxins.  What the heck do I drink then?

Fortunately, this systematic study compared the degradation of antioxidants to acrylamide and noted that acrylamide decreased more significantly than antioxidants with roasting  with antioxidants being only “slightly reduced.”  

Do this:

  • The best bet is to opt for medium to dark roasts.

The Water In The Coffee

Good, filtered water is the secret to a good cup of coffee (and beer).  Companies like Starbucks can attest to this because they use a triple-filtered reverse osmosis (RO) system.  If you’re using tap water then your coffee may contain toxins like heavy metals, pharmaceuticals, and BPA.  

I used the EWG Tap Water Database to find out that our faucet pushes out 16 contaminants above the recommended levels including arsenic, chloroform, and uranium.  Make sure your water is clean by using a good water filter. I’ll discuss this in a future article but filtering your water is very important.

We use the Waterdrop G3 Remineralization Reverse Osmosis System. Waterdrop is a reputable brand with a wide variety of filters including ones that fit on top of the counter or under the sink. If buying an RO filter seems like a bold step then at least consider a good water pitcher such as the Waterdrop Chubby pitcher which is NSF certified and has BPA-free plastic.

Do this:

  • Filter your water, ideally with a reverse osmosis (RO) filter. Read this for a deep dive into the dangers of your water.

The Coffee Maker

When scalding hot water goes through the plastic parts of a coffee maker it leaches toxins into the water which then go into your coffee.  This is another concern that often flies under the radar, however, it’s a common issue because most coffee makers are made of plastic.  

If you’re using the French Press method then you’re probably okay but if you’re reliant on the classic drip coffee maker then there’s probably plastic in your brew.  Fortunately, there are some brands that make coffee makers that make coffee makers out of stainless steel or glass.  See below.

Single-Serve Coffee Pods

Keurig and other similar coffee brands use pods (a.k.a k-cups) made of plastic and, no surprise, there are harmful contaminants in these convenient plastic pods. This study found that pods also contain BPA, BPF, benzophenone, 4-NP, DBP, and DMT (although Keurig says that their pods are BPA-free). 

The coffee in these pods also contains a toxic chemical, furan, which is linked to cancer.  This is present in many coffees as a byproduct of roasting at high temperatures but because the pod traps it, the levels tend to be higher in pods.  The tops of these coffee pods also tend to contain aluminum, however, this study said there was no increased level of aluminum in the coffee compared to other methods.

Do this Instead: 

  • A better alternative than the standard coffee pods is to use reusable stainless steel coffee pods (which are better for the environment anyway).  The best option is to just switch out your Keurig (see below)


The Coffee Filter: To Use Or Not To Use?

When coffee travels through a filter, one of the things it filters out is diterpenes.  Diterpenes, specifically cafestol and kahweol, are fatty acids with many benefits “such as anti-inflammation, hepatoprotective, anti-cancer, anti-diabetic, and anti-osteoclastogenesis activities.”  In fact, an unfiltered cup of coffee contains 30 times more diterpenes than a filtered one.   

The potential downside with diterpenes (primarily cafestol) is that they have been shown to raise serum LDL cholesterol levels.  For most people, this likely won’t be an issue but if you’re concerned with your cholesterol or have a condition such as familial hypercholesterolemia (FH) you may want to use a filter.  To get a clear picture, you can start with a 90-day test using the filter, followed by a blood test. Afterward, conduct a 90-day test without the filter and follow it up with another blood test to compare the results.

Unfiltered methods of brewing include French Press, Turkish coffee, percolator, and most cold brews and espressos.  Filtered brewing methods are pour-overs, single-cup coffee makers, and some drip coffee makers.

I use a coffee maker without a filter because my wife and I have good cholesterol levels and because unfiltered coffee provides more bitterness and a stronger flavor.

White vs. Brown Coffee Filters

The paper used for coffee filters is naturally brown but companies bleach them white to make them look nicer.  These bleached coffee filters contain dioxins and chlorine.  Dioxins have been linked to diabetes, cancer, and heart disease.

The bleaching process during manufacturing also releases chlorine compounds which are considered “the most significant environmental issue,” according to his 2012 study in Environmental Engineering and Management Journal.

Do this:

The Coffee Cup Or Container

It kills me when I see people drinking coffee from disposable cups. The downside of from a health and environmental standpoint is significant while the effort to use a reusable container is so minimal. 

Disposable cups like styrofoam and even paper cups (which basically contain a thin layer of plastic between the coffee and the paper) can contain chemicals such as styrene, BPA, formaldehyde, phthalates, vinyl chloride, and dioxin.  A report found that “BPA leaches out 55 times faster” when hot liquids interact with plastic.  On top of that, coffee is acidic and acidity also leaches toxins from non-durable containers. 

Heat + acidity + styrofoam/plastic/etc. = no beuno.

A good step up would be a mug but there’s a caveat. Make sure to avoid mugs with plastic (obviously) and decorative ceramic ones.  Decorative ceramic mugs often contain lead and cadmium.  Lead is used to make the glaze on the ceramic look shiny and smooth while the cadmium makes the designs bright. A study put these mugs in the microwave and “found a high concentration of lead and cadmium in double distilled water that leached from both old and new glazed, colourful ceramic cups.”  


In 1970 the U.S. outlawed large amounts of these toxins but small amounts remained legal.  Therefore, keep that vintage china as a decoration and avoid pulling it out for actual use.

The best options are glass, stainless steel, and non-decorative ceramic mugs. When buying a stainless steel container (for coffee or otherwise), avoid ones that have a lead solder. The inside of the container is likely unaffected but touching the outside can expose you to lead. According to the WHO, “lead is a cumulative toxicant that affects multiple body systems and is particularly harmful to young children.” There’s no safe level of lead exposure.

It should go without saying that you should also avoid plastic stirrers.  Instead, just put in whatever you're mixing your coffee with first then shake a bit.

One of my coffee-loving coworkers would embrace the mornings she could sit with a coffee mug and sip her coffee on days she wasn’t working, stressing, in a mug!  Find a non-toxic mug and follow her lead.  If you’re getting that brew to-go then bring your own container (suggestions below) or opt for a cold brew option which is less likely to leach these chemicals.

The Bottom Line


How To Choose A Healthy Cup Of Coffee

  • Use medium to dark roast organic coffee.

  • Store the beans in an airtight container that’s not exposed to light (see below).

  • Use filtered water.

  • Use a coffee maker method that uses no plastic or minimal plastic.  If you use a single-serve machine then use a reusable pod that doesn’t have plastic in it.

  • If you use a coffee filter then use a natural unbleached kind.

  • Drink coffee from a (non-ceramic) mug or a reusable coffee cup void of plastic, such as a stainless steel one.




Healthy Coffee Recommendations

Coffee Makers

Best Organic Coffee Brands

Coffee Tumblers And Mugs

Miscellaneous Coffee Stuff


If you’re going to drink that cup of coffee every day, you mind as well make some changes to make it the healthiest cup of coffee you can. Your body will thank you.





Related:

To learn more about toxins, check out The Non-Toxic Living Guidebook: Hacks, Strategies, & Natural Products for Better Health. I wrote this comprehensive guide as a way to break down the complexity of toxins into a simple, easy-to-read format with practical tips and clickable links to the least toxic products I could find. Get your copy today and use the code MBD20 at checkout for a 20% discount. You can also get the Kindle eBook on Amazon.