Preheat oven to 375 degrees F. Line a standard-size muffin tin with paper liners or spray with non-stick cooking spray.
In a small bowl, add the milk and tablespoon of vinegar and set aside for 5 minutes.In a medium bowl, whisk together the flour, ½ cup of the sugar, baking powder, nutmeg, cinnamon and salt; set aside.In a large bowl, whisk together the oil and the egg. Add the milk and vanilla extract and whisk to combine.
Add flour to wet ingredients and mix until combined being careful not to overmix. A few lumps are okay. Fold in chocolate chips.
Divide the batter evenly between the muffin cups and sprinkle the tops with sugar. Bake until golden brown and a thin knife inserted into the center comes out clean, 15 to 20 minutes.