Sift all the dry ingredients into a bowl: flour, cocoa, baking soda, baking powder and salt. Whisk or stir to blend and set aside.
In another mixing bowl, beat together the yogurt and sugar with a mixer until mixed thoroughly. Add the milk, vanilla extract and vinegar and mix until well combined.
Add the liquid to the dry ingredients and mix together well with a spatula or spoon.
Last add the hot coffee.
Spray your cupcake pan or use cupcake liners. Fill up ⅔ of the way full.
Bake at 350 degrees for 18 to 20 minutes. Allow to cool on a baking rack.
When the cupcakes are completely cool, frost as desired.
Tips for BEST Results:Make these whole wheat chocolate cupcakes on the day you plan to serve. The cupcakes definitely tasted better the first day. Whole wheat flour certainly is more dense than regular flour and I felt like by day two they were firmer. These healthy cupcakes still tasted great but had lost some of the delicateness that was there when they were fresh.The batter should be of a pourable consistency. Whole wheat flour in general require more liquid than regular all purpose flour and all wheat flours are not identical. So if your batter is too thick, you should add more milk to get it to that consistency.Use a liquid measuring cup with a pour spout to transfer the batter to the cupcake tins. It is easier to control the amount added and a much cleaner way to fill the cupcake tins.Use an electric mixer to mix the liquid ingredients incorporating air into the liquid and a fluffier cupcake.Don't skip sifting the flour and dry ingredients. This makes the mixing a bit easier so you don't over mix the batter or end up with unincorporated clumps in the cupcakes.