Preheat the oven to 350°F and lightly oil or spray a 12-cup muffin tin.
In a large bowl, combine the all-purpose and whole wheat flours, the baking powder, baking soda, salt, and nutmeg.
In a medium bowl, whisk together the yogurt, eggs, almond milk, maple syrup, olive oil, vinegar, and vanilla.
Add the wet ingredients to the bowl of dry ingredients and stir just until combined. Do not overmix. Fold in the chocolate chips and use a ⅓-cup measuring cup to scoop the batter into the muffin cups.
Bake for 22 minutes, or until the tops spring back to the touch and a toothpick inserted in the center comes out with a few crumbs attached. Let cool for 15 minutes, and then transfer to a wire rack to continue cooling.