Healthy Small Batch Mini Pumpkin Cupcakes with Chocolate Frosting
Yields: 18 mini cupcakes
These cupcakes are perfect for fall! They’re full of sweet pumpkin and warm spice flavors, and the chocolate frosting pairs so well with the pumpkin. These cupcakes are supremely moist and tender, too! They’re best if eaten the same day that they’re frosted, but leftovers will keep for at least 2 days (if not longer) if stored in an airtight container in the refrigerator.
  1. To prepare the cupcakes, preheat the oven to 350°F. Line 18 mini muffin cups with paper liners, and coat the liners with cooking spray.
  2. In a medium bowl, whisk together the flour, baking powder, baking soda, cinnamon, ginger, nutmeg, cloves, and salt. In a separate bowl, whisk together the coconut oil, egg white, vanilla, and liquid 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 9-12 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, cocoa powder, instant pudding, and liquid stevia to a large bowl. Beat with an electric hand mixer or stand 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 chocolate frosting on top just before serving.
Notes: For the gluten-free flour, use the following blend: ½ cup + 2 tablespoons (90g) millet flour, ¼ cup (30g) tapioca flour, ¼ cup (30g) brown rice flour, and ¾ teaspoon xanthan gum. Most store-bought gluten-free flour blends (like this one!) should work as well, if measured like this.

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

Remember to measure the flour, using this method or a kitchen scale. (← That’s the one I own and love!) Too much flour will dry out your batter.

For a stronger spice flavor (I always prefer stronger spice flavors!), then increase the ginger, nutmeg, and cloves by ⅛ teaspoon each (for a total of ¼ teaspoon each).

I highly recommend using the liquid 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 6 tablespoons (90mL) of agave, honey, or pure maple syrup for the liquid 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 ¼ cup of Truvia or granulated sugar.

If you’d like sweeter cupcakes, then add 2 tablespoons of this granulated erythritol (or Truvia or coconut sugar) to the cupcake batter along with the liquid stevia. I usually try to use just one sweetener to make life easier for you! However, some of my taste testers found that the pumpkin muted the liquid stevia’s sweetness. Once I added those 2 tablespoons granulated erythritol, the cupcakes tasted SO much sweeter, like true store-bought cupcakes—so I promise it’s worth using both! The baking time will increase by 1-2 minutes, if you add in the granulated erythritol.

Any milk may be substituted for the nonfat milk.

For the frosting, I’ve found that not all Greek yogurt brands are equally thick! This is my favorite one for my Greek yogurt frosting because it’s the thickest brand I’ve found, which means your chocolate frosting holds its shape so much better!

This is the instant pudding mix that I use. 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) chocolate frosting that does NOT use instant pudding (and is clean-eating friendly), use this recipe of mine.

This recipe is easily doubled to yield 12 standard size cupcakes! Remember to coat the cupcake liners with nonstick cooking spray first. Bake the standard size cupcakes 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.

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