Preheat the oven to 350 degrees F. Line one 12-muffin tin with paper liners and lightly coat with cooking spray.
Whisk the flour, baking powder and salt in a medium bowl.
Lightly whisk the eggs in a second medium bowl. Whisk in the brown sugar, sour cream, applesauce, oil and vanilla.
Gently fold the wet ingredients into the dry with a rubber spatula. Just before the batter comes together, fold in the chocolate chips (it's okay if there are lumps in the batter). Divide the batter evenly among the muffin cups. Bake until a tester inserted in the center comes out clean, 20 to 24 minutes. Let the muffins cool in the pan for a few minutes, then remove and cool completely on a rack. Store in an airtight container at room temperature for up to 3 days.
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