Line a muffin tin with liners and for best results, spray the liners with non-stick spray or spray the muffin tin with non-stick spray if not using liners.
In a medium pot, boil water and add sweet potatoes. Boil for about 20 minutes or until tender when pierced with a fork. Transfer sweet potatoes to a food processor and process until smooth. Remove lid and set aside.
Preheat oven to 400℉.
In a large bowl, add flours, cinnamon, nutmeg, baking powder, and salt. Stir until well combined.
In a separate bowl, add eggs, sugar, olive oil, and vanilla. Whisk vigorously for about one minute and ingredients are incorporated.
Add the sweet potatoes and continue to beat until batter is smooth and free of lumps.
Add the flour mixture and stir with a rubber spatula until it is evenly mixed and no flour is visible, about 50 strokes. Fold in the chocolate chips just until evenly mixed.
Spoon batter into prepared muffin tin so each cup is about 3/4 full.
Bake for 20-25 minutes or until muffins are spring back and toothpick inserted in to the center comes out clean.