Annatto seeds have dry, mild, earthy flavor, with notes of peppermint. South American and Caribbean cuisine incorporates annatto seeds/powder into many spice blends, such as adobo seasoning and recado colorado, a flavorful blend from the Yucatan peninsula. Probably the most famous traditional application is in the making of achiote paste, an important ingredient in Mexican cooking. Ground annatto seeds are combined with water, lemon juice or wine vinegar to make this paste, which is often used as a wet rub for chicken, pork and fish.

Whole annatto seeds are very hard and can be difficult to work with. Because of this, most home cooks prefer to purchase annatto in its ground form.