The Molecules Between Worlds: How Sugars and Acids Travel Through Coffee Beans
Deep inside the dense forests of Colombia, where the scent of ripe coffee cherries mixes with humid air and volcanic soil, an invisible transformation is underway.
Deep inside the dense forests of Colombia, where the scent of ripe coffee cherries mixes with humid air and volcanic soil, an invisible transformation is underway. It's not just the fermentation of mucilage that gives flavour to the world’s morning cup—it's a molecular migration, a secret voyage of acids and sugars from the outside of the bean to the inside, shaping every nuance of the brew.
This journey, meticulously documented in recent research, is changing our understanding of how flavour is born during coffee processing. The fermentation of coffee mucilage—a sticky, sugar-rich gel surrounding the beans—is often described as a surface process. But what if its influence travels further than we imagined? What if the substances formed in this microbial soup seep into the beans themselves, not just painting their exterior but altering their very core?
This question led researchers to Chinchiná, in the Colombian Andes, where the famed Castillo variety of Coffea arabicagrows. There, scientists from Cenicafé and the University of Caldas subjected coffee cherries at three stages of ripeness to extended fermentation under tightly controlled conditions. Their aim: to trace the transformation and movement of organic acids and sugars—citric, malic, quinic, acetic, tartaric, and lactic acids, as well as glucose, fructose, and sucrose—from the mucilage into the endosperm of the bean.
The results were quietly revolutionary. While citric, malic, and quinic acids appeared abundant within the bean but stable over time, tartaric and acetic acids told a different story: their concentrations rose steadily with prolonged fermentation. Using carbon isotope tracing, the researchers proved that these molecules were not just formed externally—they were diffusing into the bean.
This discovery sheds light on a fundamental mechanism in coffee processing: mass transfer by diffusion. Unlike mixing in a soup or churning of dough, this process is subtle and slow. The fermentation occurs under solid-state conditions, where the mucilage is in contact with the bean but not stirred. No convective movement. No agitation. Just a gradient of chemical potential—like a whisper carried from the outside world into the bean’s protected heart.
The implications for coffee quality are profound. Acetic acid is a double-edged sword: at low concentrations, it adds brightness and structure; at high levels, it overwhelms the palate. The ability to predict or control its migration could empower producers to fine-tune acidity. Tartaric acid, often associated with grape-like sharpness, offers similar opportunities. And sugars like fructose and glucose, while largely consumed during fermentation, leave behind metabolic residues that affect the final flavour balance.
Fermentation time and temperature emerged as the key levers. At lower temperatures, diffusion slowed—like syrup in a cool bottle. At higher temperatures, the transfer accelerated, but so did microbial activity, sometimes to destabilising effect. The challenge, then, is to strike a balance: to manage a process that is both biological and physical, both alive and molecular.
And all of this, hidden inside what we casually call “processing.”
These findings add a new dimension to the narrative of coffee flavour development. No longer can fermentation be seen only as a microbial performance on the cherry’s skin. It is a deeply chemical dialogue between the bean and its environment. For roasters, baristas, and producers alike, understanding this dialogue could unlock new levels of control—and creativity.
Because in the end, every great cup of coffee begins with a thousand invisible steps. And sometimes, the most important ones happen inside the bean.
Scientific Literature References:
Fermentation time and temperature emerged as the key levers. At lower temperatures, diffusion slowed—like syrup in a cool bottle. At higher temperatures, the transfer accelerated, but so did microbial activity, sometimes to destabilising effect. The challenge, then, is to strike a balance: to manage a process that is both biological and physical, both alive and molecular.
And all of this, hidden inside what we casually call “processing.”
These findings add a new dimension to the narrative of coffee flavour development. No longer can fermentation be seen only as a microbial performance on the cherry’s skin. It is a deeply chemical dialogue between the bean and its environment. For roasters, baristas, and producers alike, understanding this dialogue could unlock new levels of control—and creativity.
Because in the end, every great cup of coffee begins with a thousand invisible steps. And sometimes, the most important ones happen inside the bean.
Scientific Literature References:
- Osorio, V., Medina, R., Acuña, J.R., Pabón, J., Álvarez, C.I., Matallana, L.G., & Fernández-Alduenda, M.R. (2023). Transformation of organic acids and sugars in the mucilage and coffee beans during prolonged fermentation. Journal of Food Composition and Analysis, 123, 105551. https://doi.org/10.1016/j.jfca.2023.105551
- Kregiel, D., Dziekonska-Kubczak, U., Czarnecka-Chrebelska, K., & Pielech-Przybylska, K. (2025). Chemical Fingerprints of Honey Fermented by Conventional and Non-Conventional Yeasts. Molecules, 30, 2319. https://doi.org/10.3390/molecules30112319
Author:
Dr. Steffen Schwarz
Dr Steffen Schwarz is an internationally recognised expert in the field of coffee, an entrepreneur and a lecturer.
As the founder of the Coffee Consulate in Mannheim, he has for many years been dedicated to the training and further education of professionals across the entire coffee value chain. His work combines scientific insights with practical experience and covers topics such as coffee quality, sensory analysis, sustainable cultivation, and the processing and preparation of coffee.
Drawing on his many years of expertise, he advises companies worldwide, develops training programmes for the coffee industry and is committed to the responsible and quality-oriented handling of coffee. As an author, Dr Steffen Schwarz conveys complex specialist knowledge in an accessible and practical way, offering his readers new perspectives on one of the world’s most fascinating luxury foods.