Healthy Pumpkin Cupcakes with Cream Cheese Frosting

Tender spiced pumpkin cupcakes topped with gorgeous swirls of sweet cream cheese frosting. No refined flour or sugar, so easy to make & just 123 calories!
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Healthy Pumpkin Cupcakes with Cream Cheese Frosting

A couple of years ago, one of my best friends came over for an afternoon of cake decorating. I had bought Amanda’s online class (she’s the talented blogger behind I Am Baker!), and we planned to go through each of the tutorials to learn as many techniques as we could.  

Since my friend previously worked in a bakery, she already owned most of the necessary equipment (aka many tips and piping bags!), and she whipped up a big batch of buttercream ahead of time. I baked lots of cake layers and cupcakes, so when that afternoon arrived, we were totally prepared.

Healthy Pumpkin Cupcakes with Cream Cheese Frosting

We watched Amanda’s videos on how to pipe with round tips, star tips, petal tips, and more. She demonstrated rosettes, ruffles, seashells, pushed petals, Chantilly lace designs… All while making everything look so easy!

With her prior bakery experience, my friend picked up many of the piping techniques right away, but me… As an overachieving perfectionist, it took me five times as long to finally make my rosettes and pushed petals look presentable. And I ran out of time to even attempt the others!

Healthy Pumpkin Cupcakes with Cream Cheese Frosting

Learning more (and getting better!) at cake decorating is still on my baking bucket list… But for now, I’m sticking with easier endeavors, like these Healthy Pumpkin Cupcakes with Cream Cheese Frosting! They’re full of warm and fuzzy fall flavors, like sweet pumpkin and cozy spices, and those stunning swirls of delicious cream cheese frosting are much easier to achieve than you’d think!

Hint: If I can do it… I know you can too! ?

Healthy Pumpkin Cupcakes with Cream Cheese Frosting

But before I get too far ahead of myself… Let’s start with the guilt-free pumpkin cupcakes! You just need two bowls and a fork—no mixer required! Bonus points if your mixing bowls are dishwasher safe. I’m a super happy girl when there are fewer dishes to wash!

You’ll begin with white whole wheat flour (like this!), which has the exact same health benefits as regular whole wheat flour but a lighter taste and texture. That difference really helps the tender texture and sweet pumpkin flavors shine! You’ll also whisk in plenty of spices: cinnamon, ginger, nutmeg, and cloves.

Healthy Pumpkin Cupcakes with Cream Cheese Frosting

Why is it that that those spices always smell so irresistible?? Do you know? I just purchased two pumpkin spice scented candles last week… And I’m already planning on buying more. I love how their cozy smell wafts throughout my entire house!

Anyway… Moving on…

Healthy Pumpkin Cupcakes with Cream Cheese Frosting

You’ll only use a minuscule ½ tablespoon of butter or coconut oil in the entire dozen cupcakes… Because the rest of their tender texture comes from a combination of pumpkin purée (like this… not pumpkin pie mix!) and Greek yogurt. You know how much I ♡ both ingredients! Greek yogurt adds the same moisture to the batter as extra butter or oil for a fraction of the calories, and it gives your baked treats a protein boost, too!

As for the pumpkin… My blog should be renamed to “Amy’s Healthy Pumpkin Baking” every fall. It’s my favorite flavor—and I’m totally Team Pumpkin all year round! ??

Healthy Pumpkin Cupcakes with Cream Cheese Frosting

To sweeten your cupcakes, you’ll skip the refined sugar and use vanilla stevia instead, another one of my favorite ingredients. Stevia is a plant-based, no-calorie sweetener that contains nothing overly refined or artificial (aka it’s clean-eating friendly!). This is the kind I use because I love its warm flavor and don’t notice any strange aftertaste like with some other stevia products. Although many health-oriented grocery stores stock it, I buy mine online here because that’s the best price I’ve found. (And you’ll use it in all of these recipes of mine, too!)

One last thing before we move on to the frosting! You must coat your cupcake liners with cooking spray before adding in the batter. Low-fat batters stick to cupcake liners like superglue, so this nifty little trick ensures that the cupcake liners peel away just like with normal, full-fat recipes!

Healthy Pumpkin Cupcakes with Cream Cheese Frosting

Now for those gorgeous frosting swirls… ? This frosting is super simple to make! You just beat Greek yogurt, light cream cheese, more vanilla stevia, and a little instant pudding mix together in a bowl until it turns really thick and creamy. Then pop it in the fridge to chill for a few hours.

Yes, that’s it!

The instant pudding mix is what thickens the frosting to a pipe-able consistency. You can omit it… But then you’ll have to spread your frosting on top of your cupcakes instead. Just as yummy, I promise! Just not quite as stunning as those swirls!

Healthy Pumpkin Cupcakes with Cream Cheese Frosting

I’m a little embarrassed at how many of these I’ve already eaten… They’re just that good! ? And when you make your own, remember to snap a picture and share it on Instagram using #amyshealthybaking and tagging @amyshealthybaking IN the photo itself! (That guarantees I’ll see your picture! ?) I’d love to see your cupcakes and feature them in my Sunday Spotlight series!

Click here to PIN the recipe and save it for later!
Healthy Pumpkin Cupcakes with Cream Cheese Frosting
5.0 from 1 reviews

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}


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You may also like Amy’s other recipes…
   Healthy Pumpkin Cake + Cream Cheese Frosting
   Healthy Gingerbread Cupcakes + Cream Cheese Frosting
   Greek Yogurt Pumpkin Chocolate Chip Pound Cake
   Healthy Banana Cupcakes + Cream Cheese Frosting
   Healthy Pumpkin Cream Cheese Muffins
   Healthier Carrot Cake Cupcakes + Cream Cheese Frosting
   …and the rest of Amy’s healthy pumpkin recipes!

Healthy Pumpkin Cupcakes with Cream Cheese Frosting

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