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 four days (if not longer!) if stored in an airtight container in the refrigerator.

4.88 from 8 votes

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Ingredients

FOR THE CUPCAKES

2 ¼ cups (270g) white whole wheat flour or gluten-free* flour (measured like this)
2 ¾ tsp homemade pumpkin pie 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) liquid stevia
¾ cup (183g) pumpkin purée (not pumpkin pie mix!)
¼ cup (60g) plain nonfat Greek yogurt
½ cup + 2 tbsp (150mL) nonfat milk, divided

FOR THE FROSTING

1 cup (240g) plain nonfat Greek yogurt (see Notes!)
8 oz (1 block) light or fat-free cream cheese, well softened (see Notes!)
2 servings (16g) sugar-free, fat-free cheesecake instant pudding mix (see Notes!)
⅝ tsp liquid stevia (or adjusted to taste)

Instructions

To prepare the cupcakes, preheat the oven to 350°F. Line 12 muffin cups with paper liners, and coat the liners with cooking spray.
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 liquid stevia. Stir in the pumpkin purée, Greek yogurt, and 2 tablespoons of milk. Alternate between adding the flour mixture and the remaining milk, beginning and ending with the flour mixture, and stirring just until incorporated. (For best results, add the flour mixture in 3 equal parts.)
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.
While the cupcakes bake, prepare the frosting. Add the Greek yogurt, cream cheese, instant pudding, and liquid 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

IMPORTANT MEASURING NOTE – READ BEFORE BEGINNING: It's really important to measure the flour correctly, using this method or a kitchen scale. (← That’s the one I own!) Too much flour will make your cupcakes dry, instead of soft and moist.

HOMEMADE PUMPKIN PIE SPICE: For the homemade pumpkin pie 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 pie spice will also work, if you prefer.

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

STEVIA NOTES + ALTERNATIVES: Many stevia brands and products have different sweetness levels, so they're not necessarily 1-for-1 substitutes for each other. For the best results, I highly recommend using the same one that I do! It’s one of my favorite ingredients (you’ll also 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 liquid stevia AND omit the milk. (The batter should be fairly thick, similar to muffin batter.)

If you prefer not to use the liquid stevia in the frosting, then substitute 1 ½ teaspoons of this powdered stevia -OR- ¼ cup of Truvia or powdered sugar.

PUMPKIN PURÉE NOTE: Pumpkin purée is also called “100% pure pumpkin” or “canned pumpkin.” For the best results, the only ingredient on the label should be “pumpkin.” I don’t recommend substituting pumpkin pie mix because it contains other ingredients, which affects the way it behaves in baking recipes.

MILK ALTERNATIVES: Any milk may be substituted for the nonfat milk.

GREEK YOGURT NOTE: I’ve found that FAGE plain nonfat Greek yogurt works the best when making frosting because it’s thicker than many other brands, which really helps with the frosting’s consistency. (It also has less of a yogurt “tang” to its flavor!)

CREAM CHEESE NOTES: Neufchâtel cream cheese (also called reduced fat cream cheese or ⅓-less fat cream cheese), Greek yogurt cream cheese, and fat free cream cheese will all work. Regular cream cheese works well too. Whichever option you use, make sure it’s block-style (not tub-style) and well softened for the best creamy frosting consistency.

I do not recommend substituting tub-style cream cheese or whipped cream cheese. They will change the consistency of your frosting.

INSTANT PUDDING MIX NOTES: Many boxes of sugar-free, fat-free instant pudding mix have 4 servings per box. Since you only need 2 servings, you’ll use half of the box (not two boxes!).

If you can’t find sugar-free, fat-free cheesecake instant pudding mix, then substitute sugar-free, fat-free vanilla instant pudding mix instead.

Instant pudding mix is special because its thickening properties are activated when it’s cold or at room temperature — not when heated (like with cornstarch and regular “cook-and-serve” pudding mix).

Unfortunately, there isn’t a great substitute for the instant pudding mix. I’ve tried using xanthan gum, and while it does thicken the frosting, it also adds a weird texture. Regular “cook-and-serve” pudding mix and cornstarch won’t work because those require heat to activate their thickening properties, and heating the Greek yogurt is not a good idea. Therefore, for a more classic spreadable (not pipe-able) cream cheese frosting that does NOT use instant pudding (and is clean-eating friendly), use this "Frosting #1" recipe of mine.

GLUTEN-FREE OPTION: 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. Many store-bought gluten-free flour blends (I like this one from Bob's Red Mill) should work as well, if measured like this.

HOW TO STORE: Store cupcakes in an airtight container in the refrigerator. They should keep for at least four days (if not longer!).

{gluten-free, clean eating option, low fat, sugar-free, higher protein}

DID YOU MAKE THIS RECIPE?I'd love to hear what you think of it in a comment below! If you take a picture, tag @amys.healthy.baking on Instagram or use the hashtag #amyshealthybaking.