Healthy Pumpkin Cupcakes with Cream Cheese Frosting

 
A couple of years ago, one of my close 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.
 

 
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… 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!
 

 
Learning more about (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 fall flavors, like sweet pumpkin and cozy spices, and those stunning bakery-style 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! 😉
 

KEY INGREDIENTS TO MAKE HEALTHY PUMPKIN CUPCAKES

But before I get too far ahead of myself… Let’s talk about some of the ingredients you’ll need to make these healthy pumpkin cupcakes!

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 homemade pumpkin pie spice. I prefer making my own because I’ve found that many store-bought blends are fairly heavy on the cinnamon and contain minimal amounts of the other spices. They taste more bland and one-dimensional to me, whereas homemade versions have a much richer and cozier flavor — and they’re really easy to make! My blend has cinnamon, nutmeg, cloves, and ginger.

Why is it that that those spices always smell so irresistible?? Do you know? I just purchased two new 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…
 

 
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 love both ingredients! Greek yogurt and pumpkin add the same moisture to the batter as extra butter or oil but for a fraction of the calories, and the Greek yogurt gives your baked treats a protein boost, too!

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

Tip: I’ve shared 90+ healthy pumpkin-flavored recipes on my blog so far. (← You can find all of them there!) I don’t plan on stopping any time soon either!
 

 
To sweeten your cupcakes, you’ll skip the refined sugar and use liquid stevia instead. It’s 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 flavor and don’t notice any strange aftertaste like with some other stevia products. Although many health-oriented grocery stores stock it, I often buy mine online here because that’s the best price I’ve found. (You’ll use it in all of these recipes of mine, too!)

Tip: 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 liquid stevia that I do!
 

HOW TO MAKE HEALTHY PUMPKIN CUPCAKES

These healthy pumpkin cupcakes are really easy to make! You just need two bowls and a fork — and bonus points if your mixing bowls are dishwasher safe. I’m a super happy girl when I end up with fewer dishes to wash!

That’s right… I actually do not recommend using a stand mixer or hand-held mixer. Those tend to overmix batters that are low fat and sugar-free, like this one. Overmixing leads to a tough, gummy, or dense texture. However, if you gently stir by hand, your healthy pumpkin cupcakes should turn out perfectly moist and tender!

Finally, you must coat your cupcake liners with cooking spray before adding in the batter. Low fat batters stick to cupcake liners like superglue, but this nifty little trick ensures that the cupcake liners peel away just like with normal, full-fat recipes!
 

HOW TO MAKE CREAM CHEESE FROSTING

Now it’s time for those gorgeous bakery-style frosting swirls! This cream cheese frosting is super simple to make. You’ll just beat Greek yogurt, light cream cheese, more liquid stevia, and a little instant pudding mix together in a bowl until the mixture 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, buttercream-like consistency. You can omit it… But then you’ll have to spread your frosting on top of your cupcakes instead. Just as delicious, I promise! Just not quite as stunning as those bakery-style swirls.
 

 
I’m a little embarrassed to admit 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 healthy pumpkin cupcakes with cream cheese frosting!

Healthy Pumpkin Cupcakes with Cream Cheese Frosting

© Amy's Healthy Baking

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.

View Nutrition Information + Weight Watchers Points
 
 
You may also like Amy’s other recipes…
♡   Healthy Pumpkin Cake + Cream Cheese Frosting
♡   Healthy Pumpkin Oatmeal Snack Cake
♡   Healthy Pumpkin Bundt Cake
♡   Healthy Pumpkin Chocolate Chip Pound Cake
♡   Healthy Pumpkin Cream Cheese Muffins
♡   Healthy Gingerbread Cupcakes + Cream Cheese Frosting
♡   Healthy Cinnamon Apple Cupcakes
♡   Healthier Carrot Cake Cupcakes + Cream Cheese Frosting
♡   …and the rest of Amy’s healthy pumpkin recipes and cupcake recipes!