Could I swap 1/3 cup flour for cocoa?
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you could try it. it might turn out too bitter, thought, so maybe 1/3 cup of cocoa and 1/3 cup of sugar, and then as much flour as needed to make it as thick as it usually if you do the plain overnight waffles
I would suggest maybe making them a bit more simple, and adding a large handful of chocolate chips/chopped chocolate bar and folding them in just before cooking. Or reducing the sugar content and adding some chocolate syrup.
If you sub cocoa in for some flour, you will need to increase the sugar, but increasing the sugar will have the same effect of increasing the liquids, so you will also have to cut back on the liquids (not up the flour) accordingly. I would just add shaved chocolate before cooking as suggested above - much less math!
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Here is a recipe that Kitchen Butterfly posted for chocolate waffles, look at the proportions and maybe you can get an idea for your recipe.