Coffee beans are first softened in hot water or steam. Then caffeine is dissolved from the beans by using a solvent such as methylene chloride, ethyl acetate, or a gentler solvent such as water itself.
Liquid carbon dioxide is a much more expensive alternative, but has the added advantage that it does not remove the flavour molecules.

Removing caffeine from coffee

The solvents used to obtain decaf coffee also remove some of the flavour molecules. These are then added back. 
One way is to perform a first extraction with water, then shake up the water with a small volume of methylene chloride, or pass it through a charcoal filter. Both processes selectively remove the caffeine from the water but leave most of the flavour molecules.

Adding flavour molecules

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How is caffeine removed from decaf coffee?

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Caffeine is easily removed from coffee beans, however, the tricky part is making sure you don't take the flavour along with it.

By <a href="https://www.sciencefocus.com/author/lenfisher/">Len Fisher </a>

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Asked by: Katrina Parker, Durham

Caffeine is dissolved from the beans after they have been softened in hot water or steam, using either a powerful solvent such as methylene chloride or ethyl acetate, or a gentler solvent such as water itself. All of these solvents (especially the first two) remove some of the flavour molecules as well as the caffeine, though, so the trick is to find a way of putting these back.

One way is to perform a first extraction with water, then shake up the water with a small volume of methylene chloride, or to pass it through a charcoal filter. Both of these processes selectively remove the caffeine from the water, but leave most of the flavour molecules. The leftover water is then added back to the treated beans for re-absorption of the flavours.

A more expensive alternative is to use ‘supercritical’ liquid carbon dioxide as the solvent, since this dissolves the small caffeine molecules but leaves the larger flavour molecules in the beans.

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How is caffeine removed from decaf coffee? - BBC Science Focus Magazine

Removing caffeine from coffee

Adding flavour molecules

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