Healthy Pumpkin Cupcakes with Cream Cheese Frosting
Yields: 12 cupcakes
These cupcakes are perfect for fall—and for any pumpkin lover! The cupcakes are incredibly tender and full of cozy spices, then topped with stunning swirls of sweet cream cheese frosting. With how incredible they taste, you just might find yourself reaching for another! (I certainly did!) They’re best if eaten the same day they’re frosted, but any leftover cupcakes will keep for at least one week if stored in an airtight container in the refrigerator.
  • for the cupcakes
  • 2 ¼ cups (270g) white whole wheat flour or gluten-free* flour (measured like this)
  • 2 ¾ tsp homemade pumpkin spice (see Notes)
  • 1 ½ tsp baking powder
  • ¾ tsp baking soda
  • ½ tsp salt
  • ½ tbsp (7g) coconut oil or unsalted butter, melted
  • 2 large egg whites, room temperature
  • 2 tsp vanilla extract
  • 1 tbsp (15mL) vanilla stevia
  • ¾ cup (183g) pumpkin purée (not pumpkin pie mix!)
  • ¼ cup (60g) plain nonfat Greek yogurt
  • 10 tbsp (150mL) nonfat milk
  • for the frosting
  • 1 cup (240g) plain nonfat Greek yogurt
  • 8 oz (1 block) light or fat-free cream cheese, well softened
  • 2 servings (16g) sugar-free, fat-free instant cheesecake pudding mix (see Notes)
  • ⅝ tsp vanilla stevia, or adjusted to taste
  1. To prepare the cupcakes, preheat the oven to 350°F. Line 12 muffin cups with paper liners, and coat the liners with cooking spray.
  2. In a medium bowl, whisk together the flour, pumpkin spice, baking powder, baking soda, and salt. In a separate bowl, whisk together the coconut oil, egg whites, vanilla, and vanilla stevia. Stir in the pumpkin purée and Greek yogurt. Alternate between adding the flour mixture and the milk, beginning and ending with the flour mixture, and stirring just until incorporated. (For best results, add the flour mixture in 3 equal parts.)
  3. Divide the batter between the prepared paper liners. Bake at 350°F for 19-21 minutes or until the centers feel firm to the touch and a toothpick inserted into the center comes out clean. Cool in the pan for 5 minutes before transferring to a wire rack to cool completely.
  4. While the cupcakes bake, prepare the frosting. Add the Greek yogurt, cream cheese, instant pudding, and vanilla stevia to a large bowl. Beat with an electric mixer for 2 minutes. Cover the top of the bowl with foil, and refrigerate for at least 2 hours. Once the cupcakes have completely cooled, pipe the cream cheese frosting on top just before serving.
Notes: For the gluten-free flour, use the following blend: 1 cup (120g) millet flour, ¾ cup (90g) tapioca flour, ½ cup (60g) brown rice flour, and 1 ½ teaspoons xanthan gum. Most store-bought gluten-free flour blends should work as well, if measured like this.

Whole wheat pastry flour, regular whole wheat flour or all-purpose flour may be substituted for the white whole wheat flour.

For the homemade pumpkin spice, use as follows: 1 ¾ teaspoons ground cinnamon, ½ teaspoon ground ginger, ¼ teaspoon ground nutmeg, and ¼ teaspoon ground cloves. Store-bought pumpkin spice will also work, if you prefer.

I highly recommend using the vanilla stevia! It’s one of my favorite ingredients (you’ll use it in all of these recipes of mine!), and I buy it online here because that’s the cheapest price I’ve found. If you prefer not to use stevia in the cupcakes, substitute ¾ cup (180mL) of agave, honey, or pure maple syrup for the vanilla stevia. Omit the milk. (The batter should be fairly thick, similar to muffin batter.) If you prefer not to use the vanilla stevia in the frosting, then substitute 1 ½ teaspoons of this powdered stevia OR ¼ cup of Truvia or granulated sugar.

Any milk may be substituted for the nonfat milk.

You just need the dry instant pudding mix—don’t prepare it according to the package directions! For a more classic spreadable (not pipe-able) cream cheese frosting that does NOT use instant pudding (and is clean-eating friendly), use this recipe of mine.

{gluten-free, clean eating option, low fat, lower sugar, higher protein}
Recipe by Amy's Healthy Baking at