A Pod, a Bar, and Everything In Between

The journey from cocoa pod to chocolate bar is long, messy, and crucial to shaping the taste of the world’s favorite sweet.  

A new study has untangled how microbes, temperature, and pH levels during cocoa bean fermentation influence the final flavor, offering a roadmap for more consistent, high-quality chocolate. 

“Fermentation is a natural, microbe-driven process that typically takes place directly on cocoa farms, where harvested beans are piled in boxes, heaps, or baskets,” explained lead author David Gopaulchan in a statement. “In these settings, naturally occurring bacteria and fungi from the surrounding environment break down the beans, producing key chemical compounds that underpin chocolate’s final taste and aroma. However, this spontaneous fermentation is largely uncontrolled.” 

Working with women-owned farms in Colombia, Gopaulchan and his team measured microbial activity, temperature, and pH during fermentation. They found predictable successions: yeasts such as Saccharomyces cerevisiae arrive first, breaking down sugars and raising heat.  

Temperatures then spike within 24 hours, and by 48 hours, acetic acid and lactic acid bacteria take over, turning alcohol into acids that alter the beans’ chemistry. The timing of these microbial shifts strongly shapes flavor. 

The researchers catalogued microbial genes tied to desirable flavor compounds and then re-created the process in the lab with curated microbial “starter cultures.” Chocolate expert tasters reported that the lab-fermented beans reproduced fine chocolate notes such as citrus, berry, and orange blossom.  

Gopaulchan hailed the findings as they will help chocolate producers to maximize their cocoa crops and achieve great flavors through “a standardized, science-driven process.” 

“Just as starter cultures revolutionized beer and cheese production, cocoa fermentation is poised for its own transformation,” he said in the statement. “…This work lays the foundation for a new era in chocolate production, where defined starter cultures can standardize fermentation, unlock novel flavor possibilities, and elevate chocolate quality on a global scale.” 

But not everyone is convinced: Craft chocolate makers warned that standardized cultures risk homogenizing flavor and undermining farming practices.  

“Good farming practices already produce great tasting chocolate,” Luisa Bedi and Martyn O’Dare of Luisa’s Vegan Chocolates, told Science News.  

Others questioned whether the standardized microbial mixture would outperform native yeasts and bacteria. 

“Humans have a very sharp boundary for what tastes really good and what tastes awful,” yeast geneticist Aimee Dudley, who was not involved in the study, told Science News. “And the yeast make the amount of those compounds at exactly that boundary of what humans think is palatable.”