By breaking down indigestible chocolate compounds and fermenting cocoa fibre, they generate a potent anti-inflammatory effect.
It is this, scientists believe, that helps to protect the heart and arteries from damage.
Maria Moore, from Louisiana State University said: "We found that there are two kinds of microbes in the gut: the 'good' ones and the 'bad' ones.
"The good microbes, such as Bifidobacterium and lactic acid bacteria, feast on chocolate.
"When you eat dark chocolate, they grow and ferment it, producing compounds that are anti-inflammatory."
However, she added that "bad" gut bacteria, such as Clostridia and some strains of Escherichia coli (E.coli) help to trigger inflammation.
The team tested three types of cocoa powder, the raw ingredient used to make chocolate, in an artificial digestive tract consisting of a series of modified test tubes.
Cocoa contains antioxidant polyphenol compounds such as catechin and epicatechin and a small amount of dietary fibre.
Both components are poorly digested and absorbed, but are readily processed by the friendly bacteria in the colon.
"In our study we found that the fibre is fermented and the large polyphenolic polymers are metabolised to smaller molecules, which are more easily absorbed," said Dr John Finley, who led the Louisiana team.
"These smaller polymers exhibit anti-inflammatory activity. When these compounds are absorbed by the body, they lessen the inflammation of cardiovascular tissue, reducing the long-term risk of stroke."