Healthy Blueberry Cupcakes with Cream Cheese Frosting {Recipe Video!} | Amy's Healthy Baking (2024)

Tender vanilla cupcakes full of juicy blueberries & topped with dreamy swirls of sweet cream cheese frosting. No butter, refined flour or sugar & only 130 calories!


In mid-June, I dropped my mom off at the airport one Monday for her evening flight back home. After our jam-packed weekend, I completely lacked the energy to cook, so I stopped by Panera on my way back to grab a healthy salad.

Upon ordering, I sat down on a cushioned bench in their lobby to wait for my takeout meal. While the restaurant staff tossed together my fresh vegetables and lettuce, I scribbled down a quick shopping list, planning to stop by the grocery store across the street before driving home.


With just a few minutes before my stomach started growling as loudly as an airplane engine during takeoff, I quickly strode into the store, intending to power walk to the baking aisle and leave less than 5 minutes later, but…

The fresh produce display caught my eye as soon as I entered the store. “$0.99 per pint of blueberries!” shouted the bright yellow sale sign. With their plump and juicy appearance, it seemed a shame to pass them by… So I grabbed three packages and brainstormed what to make as I finished my grocery shopping.


After how deliciously these cupcakes turned out last week, I immediately decided to bake another flavor—and these Healthy Blueberry Cupcakes with Cream Cheese Frosting were the result! The incredibly sweet and juicy berries pair perfectly with the ever-so-slightly tangy frosting… And with no butter, refined flour or sugar and only 130 calories, they truly taste like a dream come true!

Even better? They’re supremely easy to make! You can see how in my video below!


And before you get started, let’s go over a few key ingredients… Starting with the white whole wheat flour (like this!). Yes, such a thing actually exists! It’s made by finely grinding a special type of soft white wheat (hence the name!), whereas regular whole wheat flour comes from a heartier variety of red wheat. White whole wheat flour has a lighter taste and texture, similar to all purpose flour’s, but it still has the same health benefits (like extra fiber and nutrients!) as regular whole wheat flour.

Note: I included my favorite gluten-free substitute in the Notes section of the recipe, if you prefer!

With only 1 tablespoon of coconut oil, the rest of these cupcakes’ tender texture comes from Greek yogurt. It’s a true magician in baking recipes! Greek yogurt provides the same moisture as extra butter or oil for a fraction of the calories, and it gives your cupcakes a protein boost, too!


Then you’ll use one of my favorite ingredients to sweeten them: liquid stevia. Stevia is a plant-based, no-calorie sweetener, and it contains nothing refined or artificial (which makes it clean-eating friendly!). This is the kind I use because I love its sweet flavor and don’t detect any strange aftertaste. Although many health-oriented grocery stores stock it, I buy mine online here because that’s the cheapest price I’ve found. (And you’ll use it in all of these recipes of mine, too!)

Before dolloping your batter into the pan, remember to coat your cupcake liners with cooking spray! Low-fat batter sticks to liners like superglue, so this nifty trick ensures the liners peel away from your cupcakes just like normal—without half of your cupcake stuck to it!


And now for the frosting… It’s a mix of more Greek yogurt, light cream cheese, a little more liquid stevia, and instant pudding mix. I know it sounds strange, but this instant pudding mix is a key ingredient! It makes the frosting stiff enough to pipe on top of your cupcakes in beautiful chic swirls.

Hint: If you can’t find this instant pudding mix, then use this cream cheese frosting recipe of mine instead!


Excited to make your own dreamy cupcakes? 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 blueberry cupcakes!

Healthy Blueberry Cupcakes with Cream Cheese Frosting {Recipe Video!}

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Yields: 12 cupcakes

These cupcakes taste like the epitome of summer! Sweet, plump, juicy blueberries… Tender vanilla cake… Dreamy swirls of cream cheese frosting… What’s not to love?? The frosted cupcakes will keep for at least three days if stored in an airtight container in the refrigerator. The frosting can be made up to a week in advance if stored in an airtight container in the refrigerator.

  • for the cupcakes
  • 2 cups (240g) white whole wheat flour or gluten-free* flour (measured like this)
  • 1 ½ tsp baking powder
  • ½ tsp baking soda
  • ½ tsp salt
  • 1 tbsp (14g) coconut oil or unsalted butter, melted
  • 2 large egg whites, room temperature
  • 2 tsp vanilla extract
  • 2 ¾ tsp liquid stevia
  • ½ cup (120g) plain nonfat Greek yogurt
  • ¾ cup (180mL) nonfat milk
  • 1 cup (140g) fresh blueberries

  • 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 liquid 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, baking powder, baking soda, and salt. In a separate bowl, whisk together the coconut oil, egg whites, vanilla, and liquid stevia. Stir in the 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 4 equal parts.) Gently fold in the blueberries.
  3. Divide the batter between the prepared paper liners. Bake at 350°F for 18-21 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 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: For the gluten-free flour, use the following blend: 1 cup (120g) millet flour, ½ cup (60g) 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.

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 ¾ cup (180mL) 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 liquid 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.

Frozen blueberries may be substituted for the fresh, although they will stain the batter a light gray color, and the baking time will increase slightly.

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, low sugar}

View Nutrition Information + Weight Watchers Points


You may also like Amy’s other recipes…
Healthy Banana Cupcakes with Cream Cheese Frosting
The Ultimate Healthy Dark Chocolate Cupcakes
Healthy Carrot Cake Cupcakes with Cream Cheese Frosting
Healthy Mini Dark Chocolate Banana Cupcakes
Healthy Gingerbread Cupcakes with Cream Cheese Frosting
Healthy Lemon Cupcakes with Raspberry Vanilla Frosting
Greek Yogurt Blueberry Lemon Pound Cake

Healthy Blueberry Cupcakes with Cream Cheese Frosting {Recipe Video!} | Amy's Healthy Baking (2024)
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