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Red and Black Quinoa are very similar in flavor. Both have a lovely 'nutty' quality, and are slightly higher in antioxidants (anthocyanin) than regular pearl quinoa. You should have no difficulty using different types of quinoas in your favorite recipes, as their cooking times do not typically differ.
Sprouted Quinoa on the other hand is considered to be slightly faster cooking and higher in some enzymes due to the sprouting process. It also is noted in having a 'slightly sweet', 'nutty' flavor.
The above answer is correct, quinoa really tastes the same no matter what color.
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There is actually a slight but subtle difference in flavor, but using different colors can make the plate more appealing to the eye. I like to stuff roasted red peppers with black quinoa. One of my friends who I've turned into a quinoaholic noticed the difference in flavor right away.
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