"This coffee has good acidity." "This one is sour and no good." With the same word, acid, we make opposite judgements. That is not a contradiction. Good acidity and bad acidity are chemically different substances.
(Research block: from here on, published data.)
Thirty-eight organic acids have been identified in roasted coffee (Yeager et al., 2021). In green coffee the leading acids are citric, malic and quinic. Roasting creates new ones: acetic, formic, lactic and others. So in one cup, acids from the farm, from fermentation and from roasting sit side by side.
Here is a surprising study. In an experiment comparing the concentrations of organic acids in brewed coffee with sensory thresholds, the only acid present above its detection threshold was citric acid; malic, acetic and lactic acids sat around threshold. And even coffee professionals could not correctly identify single acids at cup concentrations (Rune et al., 2023). So "this apple-like acidity is malic acid" is a metaphor, not an analysis. I think the industry, ourselves included, should admit this frankly.
Still, the composition of acids corresponds to taste. Even if single acids cannot be identified, the balance of the whole composition creates the impression. In good fermentation, lactic, citric and malic acids are in order; in bad fermentation, excess acetic acid and butyric and propionic acids appear (Martins et al., 2019).
Butyric acid smells of cheese or vomit; propionic acid of onion. These two are markers of over-fermentation and are not detected in a sound fermentation (Martins et al., 2019). Acetic acid in moderation contributes brightness, but in excess becomes vinegar. And the accumulation of acetic acid correlates with high temperatures (Lee et al., 2023).
In short, most bad acids are born of failed control of temperature and time. We manage fermentation by pH and temperature to prevent exactly these accidents. Good acid is made on purpose; bad acid leaks out of carelessness.

Fermentation is the process of turning sugar into acid. In an experiment measuring mucilage fermentation, acidity nearly doubled while Brix fell from 15.8 to 8.45 (Plaza-Dorado et al., 2024). How far to grow the acid, how much sweetness to keep. Deciding when to stop fermentation is deciding this balance.
One more thing, not widely known. The calcium and magnesium content of water has been reported to change how much organic acid is extracted (a 2024 GC-MS/NMR study). Brew the same beans with the same recipe, and water of a different hardness gives a different expression of acidity. One reason for "same beans as the café, different taste" is the water.
Please do not be afraid of acidity; that is what I really want to say. The acid in coffee is proof of fruit and proof of good fermentation. What to avoid is not acid itself but acid whose management failed. And you can tell them apart well enough by whether the cup is unpleasant. Acid with sweetness is quality; acid that stabs the tongue is an accident. That is all you need to remember.
The strength of perceived acidity and irritation of the stomach do not necessarily coincide. Perceived acidity is mainly a matter of the type and balance of organic acids, and the pH itself is in a mild range for a food.
It is a metaphor. In research, even professionals could not identify single organic acids at cup concentrations. But there is a correspondence between acid composition and impression, so as a description it is useful.
Mostly from failed fermentation control: excess acetic acid from hot fermentation, butyric and propionic acids from over-fermentation, and so on. It can be prevented by managing temperature and time.
For bean-side sourness, see The other reason your coffee is sour; for fermentation and the formation of acids, Fermentation time and organic acids; for temperature, What lowering fermentation temperature by 1 °C means.
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