I used to make and sell chocolate chunk cookies to several dessert shops. I never had discoloration. I have to think it's the chocolate that you are using? I used Ghirardelli Bittersweet Chunks. Maybe try using a different chunk.
If the discoloration is chocolate, it's not really a problem. I believe that commercial chocolate chips are made to be more stable in the oven, so you could switch to those if it bothers you.
Hi, that has happened to me a few times, I haven't a quick fix, however, found this link something to ponder: http://humantouchofchemistry.com/why-does-chocolate-turn-grey-sometimes-is-it-still-safe-to-eat.htm
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