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1
Preheat oven to 300 F. Line 14 regular-size muffin tins or 36 mini muffin tins with paper liners or generously grease with oil or butter.
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2
In a large bowl, beat the eggs until foamy and light yellow, a minute or so. Add the yogurt, canola oil, sugar, and vanilla and beat again until one even color and consistency, another minute. Set aside. You can also do this with a whisk and a little elbow grease.
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3
In a medium bowl, combine the whole-wheat pastry flour, all-purpose flour, cocoa powder, cinnamon, baking soda, and salt. Stir well with a fork to blend all the ingredients.
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4
Add the dry ingredients to the wet and use a rubber spatula to gently combine the two just until evenly mixed together.
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5
Be sure to squeeze the zucchini firmly in your hand or press down in a colander to release excess liquid before measuring it. Add zucchini and chocolate chips to the batter. Stir gently until just combined.
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6
For full-size cupcakes, fill each tin with 1/4 cup of batter. For mini cupcakes, figure about 1 1/2 tablespoons of batter each (although this can vary depending on the size of your muffin tins).
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7
Put into the oven and bake until a toothpick inserted into the center comes out clean, 25 to 28 minutes for full-size cupcakes, closer to 20 minutes for minis.
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8
Remove from oven and leave on the counter in the pan until completely cool. Finish with a light dusting of confectioners' sugar or your favorite chocolate frosting.
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9
Will keep up to 4 days in the fridge or wrapped well, will freeze for up to 1 month.
