Science of Coffee: The changing chemistry of coffee beans from farm to cup

Roasting at Peace Coffee // Photo by Tj Turner

This feature was underwritten by Peace Coffee. The Growler maintained full editorial control of the content.

In modern America, nothing appears more ordinary than a cup of coffee.

Coffee is available at gas stations and fast food joints; it’s made in our homes and offices; it’s consumed in upscale cafes and restaurants. Its price and pedigree vary wildly, but all coffee is, despite its everyday nature, basically a liquid miracle. Each cup is a confluence of complex chemical and biological processes that transform a simple seed into a beverage of infinite variety.

It takes dozens of individual steps to bring coffee from the field to your mug, but there are three main events that turn the bean into the liquid so many of us rely upon. The first is processing at the country of origin, the second is roasting, and the third and final event is brewing.

Parchment coffee laid out to dry before having the skin or parchment removed from the bean at the Sopacdi Cooperative in South Kivu, Democratic Republic of Congo // Photo courtesy Peace Coffee


There are numerous ways to process coffee beans, but the end goal is the same: separate the beans from the coffee fruit, use fermentation to break down the tough mucilage that connects each pair of beans to each other, and then dry the beans out so they’re resistant to spoilage and ready to ship.

Most coffee is processed according to local traditions and resources, and while it’s an easy step to overlook as a consumer, it plays a significant role in coffee’s final flavor.

Ripe coffee cherries at the AIEPEP Cooperative in Pumiri, Caranavi, Bolivia // Photo courtesy Peace Coffee

“A classic example of this is eastern versus western Ethiopia,” says Jackson O’Brien. O’Brien is the head barista for Peace Coffee in Minneapolis, where he works to set standards for the company’s cafe drinks and train incoming baristas. Heavy rainfall in the southwestern part of Ethiopia, says O’Brien, means that the Oromo and Sidamo-speaking regions have plenty of clean water available with which to do a wet (or “washed”) process coffee.

“Because the water is plentiful, you’re going to wash that fruit pulp off [of the bean],” he says. “But you also want to make sure that sun-drying process happens as fast as possible because it might rain during the drying process.

By contrast, O’Brien says, coffee in the arid eastern part of Ethiopia tends to be dry-processed, with whole cherries dried in the sun until they can be hulled at a mill later. “You get these really pungent fruit flavors and almost kind of ferment-y, winey flavors at times, while the western Ethiopian coffees are going to be a lot cleaner and have a kind of citrusy, lemony, black tea kind of flavor. Both of those regions prize that uniqueness about their coffee, and they’re really born out of local chemistry.”

A third, semi-dry (or “honey”) process is often used by Central and South American producers and in Indonesia. Skin and pulp are removed from the cherry, but some or all of the mucilage remains to be dried along with the bean.

Historically, the processing of coffee at origin has been a largely rote affair—you take advantage of the resources you have on site (ample sun and/or plenty of fresh water) and get the beans down to 12–15 percent moisture content so that they’re ready to be shipped and roasted. But in recent years, the coffee industry has begun tapping into the fermentation aspects of coffee processing to take maximum advantage of beans’ unique potentials.

“There’s a micro-mill in Costa Rica called Las Lajas, and every year they do five different processes on the coffee they get in-house,” says O’Brien. “They all taste remarkably different even though they’re all grown in the same relative elevation and they’re the same varieties going into it.”

The fickle nature of fermentation’s microfauna plays a bigger role in coffee than even many coffee industry people understand. Duluth Coffee Company founder Eric Faust recalls buying a Colombian coffee of an unknown varietal two years ago and being blown away by the flavor. “We bought it, and then the next year we bought it again and we were like, ‘This is not nearly as good as it was the year before.’

“The year before it cupped at 92–94 points; the next year it was 85,” he continues. “When we were in Colombia in February we were talking to the exporter and he said, ‘Yeah, after [the grower] received all that money for that coffee, he took out his wooden fermentation tank and put in a stainless steel one and that totally changed the coffee.’”

Roasted beans at Peace Coffee dropping from the roaster to be cooled // Photo by Tj Turner


Once coffee beans have been removed from the fruit, fermented, and dried for shipment, the next stop is typically a roastery, where the beans are stirred constantly and blasted with heat to create the brownish, ready-to-grind little nuggets we’re familiar with.

Roasting accomplishes two main things: it evens out the moisture content of the beans so that they’re ready for further roasting and flavor development, and it creates caramelization that helps balance coffee’s bitter flavors with sweetness. Knowing how far to take a given coffee is the art of roasting.

Freshly roasted beans being organized by weight before being sent to packaging // Photo by Tj Turner

“Those same marvelous fruit notes that are present in those two Ethiopian coffees that I mentioned—if you under-roast it, no matter what the coffee is, it’s going to taste grassy, and vegetal, and kind of sour and unpleasant,” says O’Brien.

But by that same token, light roasts can help show off the distinctive character of a particular bean. “Light roast coffees help highlight nuances since you aren’t just getting these burnt, roasty, deep chocolate flavors,” says Michelle Johnson. Johnson is the creator of The Chocolate Barista, a blog dedicated to furthering racial diversity in the coffee industry. “You’re letting the bean do its own thing and show off the prettier aspects—the acid, the sweetness, and all of these things are directly correlated to how you fermented the coffee, how you dried it—all of that.”

And while darker roasts can obscure those nuances, that’s not always a bad thing, says O’Brien. “If you have a coffee that has a rotten fruit character to it, which some dry processed coffees might have, you might want to mute that by taking it to a deeper [roast] level.”

Careful roasting is one of the keys to the business. For Faust, it’s a tool to create balance in the finished brewed cup of coffee at the end of the process. “We as a company have moved to only single-origin coffees,” he says. “I appreciate trying to tap into the natural terroir of a coffee. Also as a roaster I don’t feel like I need to blend [beans]—I feel like I’m able to blend in the process of roasting.”

That balance of bitter and sweet that roasting can impart is something, Faust says, that experts and casual coffee drinkers can both appreciate. “When someone tastes a cup of coffee, they might not say, ‘this tastes like cashews,’ or macadamia nuts, or stone fruits…they might just say, ‘ah, this is good, it’s smooth.’ That’s balance.”

Photo by Tj Turner


There are a lot of right ways to brew a cup of coffee. There are also plenty of ways to screw it up. What even coffee professionals acknowledge is that when it comes to creating an ideal cup, the process is at least as much art as it is science.

“There’s still a lot that’s unknown as far as hard science goes,” says O’Brien. “We know that there are some 900 different chemical compounds present in coffee and a lot of them are soluble in water. They all dissolve at slightly different rates. The good thing for us is that the worst-tasting of those compounds are typically the last things to dissolve. Brewing coffee is a lot like playing blackjack or the Price is Right—you want to get as much as possible out of that bean without going over.”

Coffee fanatics all have their favorite methods. Pour-over coffee (think Chemex) is very much in vogue, but espresso isn’t going anywhere and there are plenty of coffees where a method like a French press can soften acidity to create a great cup.

The brewing process is a symphony of inputs. “You have a small window of trying to achieve the best flavors possible,” says Johnson. “There are a few different variables that will help you achieve your final cup. There’s the temperature of the hot water, there’s grind size, agitation…if you’re brewing espresso, pressure is a part of it. And time, of course.”

And often overlooked when it comes to brewing a perfect cup of coffee: water. “The final cup of coffee is 98-percent water and only 2-percent what was in the coffee bean,” says Johnson. “In Phoenix, the tap water is horrible and it has a lot of calcium in it. You can brew a cup of coffee with that water, but because of all the calcium it’ll taste muddled and have a milk sort of texture and mouthfeel to the final cup.”

All the different inputs that go into creating ready-to-brew coffee beans—the growing, the processing, and the roasting—means that there isn’t really a one-size-fits-all answer for brewing.

“Everyone wants to know how to brew the perfect cup—what’s the ratio,” says Faust. “I think people should trust their own tastebuds. Ultimately it’s about what tastes good to you.”

Peace Coffee began in 1996 with a mission to make exceptional tasting, organic and fair trade coffee. As a Certified B Corporation located in the heart of Minneapolis, Peace Coffee is dedicated to paying small-scale farmers industry-leading prices and offering staff competitive wages with supportive benefits. Named one of the top 10 most sustainable coffee companies in the country by Civil Eats, Peace Coffee is poised to continue to fulfill its mission while delighting taste buds across the upper Midwest.