Cupcakes so healthy you could eat for breakfast?! Yes, please! No butter, oil or refined sugar in these Healthy Whole Wheat Blueberry Cupcakes that are bursting with blueberries and topped with a dreamy, creamy maple cream cheese frosting.

Healthier Cupcakes!
These Whole Wheat Blueberry Cupcakes are hearty from whole wheat flour and bursting with juicy blueberries. They’re lightly sweetened with maple syrup and are sure to satisfy when topped with the dreamy frosting that’s made with cream cheese, Greek yogurt and maple syrup. You won’t miss the butter, oil, or refined sugar that most cupcakes are filled with.

Filling and Fabulous
These cupcakes have all the health and heartiness of a muffin, but since they’re frosted, we’re calling these cupcakes and we’re eating them for breakfast or any time of the day, okay?! Of course, my blueberry streusel muffins, blueberry banana muffins, and my blueberry swirl muffins make some pretty amazing blueberry treats. But these cupcakes are…something special.
One of these cupcakes for breakfast or for a mid-day snack along with a cup of hot coffee or a big glass of fresh orange juice will have you feeling great and energized to conquer the day. They’re filling and fabulous!

Simple and Perfect
The batter consists of simple ingredients that you probably always have on hand. And the best is seeing how some of the blueberries will burst as the cupcakes bake. The frosting is lightly sweet and oh so simple, turns out perfectly creamy and complements these healthy cupcakes so well.
I can’t get over how great these cupcakes taste for how healthy they are! They’re so easy to make and keep great in the fridge for a week full of blueberry bliss.

Ingredients and Supplies
(see recipe card at the bottom of this post for measurements and details. To learn more about specific baking ingredients and how they function in baking recipes, reference my Complete Guide to Baking Ingredients)
Ingredients:
- Whole wheat flour: adds fiber and structure while keeping the cupcakes tender and wholesome. Whole wheat flour adds a heartier texture and more nutritional value over all-purpose white flour. You can sub white whole wheat flour for a lighter texture.
- Baking powder: leavening agent that makes the cupcakes rise and become fluffy.
- Baking soda: leavening agent that gives the cupcakes lift and tenderness.
- Ground cinnamon: adds warm, comforting flavor that complements the maple and blueberry so well.
- Kosher salt: balances the sweetness and enhances the other flavors. Table salt will actually pack a saltier punch than Kosher salt so if you only have table salt, adjust accordingly.
- Large eggs: binds the batter and contribute moisture and richness.
- Milk: adds moisture and helps create a smooth, pourable batter. I use nonfat milk, but you can use your favorite.
- Maple syrup: naturally sweetens the cupcakes while adding subtle flavor depth. You can substitute the maple syrup with honey, agave or date syrup, if desired.
- Pure vanilla extract: boosts the overall flavor with a warm, sweet note.
- Fresh blueberries or frozen blueberries: provide juicy bursts of sweetness and add natural color and nutrition.
- Cream cheese: gives the frosting its creamy, tangy base.
- Plain Greek yogurt: lightens the texture of the frosting while adding a bit of tang and boosting the protein. You can use a whole milk or non-fat Greek yogurt.
Supplies:
- 12-cup muffin pan
- Cupcake liners
- Nonstick cooking spray
- Large mixing bowl
- Whisk
- Spatula or wooden spoon
- Electric stand mixer or hand mixer

How to Make Whole Wheat Blueberry Cupcakes
- Preheat oven to 350°F. Line a 12-cup cupcake pan with cupcake liners and spray with non-stick cooking spray.
- In a large mixing bowl, whisk together the flour, baking powder, baking soda, cinnamon and salt.
- Make a well in the center of the flour mixture and add the eggs, milk, maple syrup and vanilla. Whisk until mixture is thick and well combined.

- Gently fold in the blueberries with a spatula or wooden spoon.
- Divide mixture evenly among prepared cupcake liners, filling each one about 2/3 full.
- Bake for 13-15 minutes or until a toothpick inserted in the center of the cupcakes comes out with a few crumbs on it.
- Let cupcakes cool in pan for 10 minutes before transferring to a wire rack to cool completely.

- To make the frosting, add the cream cheese, Greek yogurt and maple syrup to the bowl of an electric mixer fitted with a whisk attachment (or use a hand mixer and a bowl).

- Beat on medium speed until smooth and spreadable, scraping the sides of the bowl as needed.

- Once cupcakes are cool, frost each cupcake with the maple cream cheese frosting. Garnish with a blueberry, if desired.

Storage
Once frosted, store the cupcakes in an airtight container in the refrigerator for up to 4 days. Let them come to room temperature before serving for the best flavor and texture.
To freeze, skip the frosting and let the baked cupcakes cool completely. Wrap each one tightly in plastic wrap and place in a freezer-safe bag or container. They’ll keep well for up to 3 months. Thaw at room temperature or warm gently in the microwave.
You can totally enjoy these cupcakes without the frosting as wholesome blueberry muffins! Just follow the same baking instructions and store them at room temperature in a sealed container for up to 3 days or in the refrigerator for up to 6 days.

More Marvelous Muffins
Sweet or savory, indulgent or healthy, discover your new favorite snack in my Marvelous Muffin Recipes!

If you make my Healthy Whole Wheat Blueberry Cupcakes and post a pic to social, be sure to tag me on Instagram @thebakermama so I can see! If you’re on Facebook, be sure to join my Friends of The BakerMama group to connect and share all the fun and yummy recipes of mine that you make! 😍 I just love seeing how inspired and creative y’all get with the ideas I share. Enjoy!
xoxo,

Healthy Whole Wheat Blueberry Cupcakes
- Prep Time: 10 mins
- Cook Time: 15 mins
- Total Time: 25 mins
- Yield: 12
- Category: Breakfast
Description
No butter, oil or refined sugar in these Healthy Whole Wheat Blueberry Cupcakes that are bursting with blueberries and topped with a dreamy, creamy maple cream cheese frosting.
Ingredients
Cupcakes:
- 2 cups whole wheat flour
- 1 teaspoon baking powder
- 1 teaspoon baking soda
- 1 teaspoon cinnamon
- 1/4 teaspoon kosher salt
- 2 large eggs, lightly beaten
- 1 cup milk
- 1/2 cup pure maple syrup
- 1 teaspoon vanilla
- 1 and 1/2 cups fresh or frozen blueberries
Maple Cream Cheese Frosting:
- 1 (8 ounce) package cream cheese, softened (I use 1/3 less fat cream cheese)
- 3 tablespoons plain or vanilla-flavored Greek yogurt
- 2 tablespoons pure maple syrup
Instructions
- Preheat oven to 350°F. Line a 12-cup cupcake pan with cupcake liners and spray with non-stick cooking spray.
- In a large mixing bowl, whisk together the flour, baking powder, baking soda, cinnamon and salt. Make a well in the center of the flour mixture and add the eggs, milk, maple syrup and vanilla. Whisk until mixture is thick and well combined. Gently fold in the blueberries with a spatula or wooden spoon.
- Divide mixture evenly among prepared cupcake liners, filling each one about 2/3 full. Bake for 13-15 minutes or until a toothpick inserted in the center of the cupcakes comes out with a few crumbs on it. Let cupcakes cool in pan for 10 minutes before transferring to a wire rack to cool completely.
- To make the frosting, beat the cream cheese, Greek yogurt and maple syrup with a hand mixer (or in the bowl of an electric mixer fitted with the whisk attachment) on medium speed until smooth and spreadable, scraping the sides of the bowl as needed.
- Once cupcakes are cool, frost each cupcake with the maple cream cheese frosting.














I made these over the weekend and made a couple adjustments based on what I had available: I used 1/4 cup maple syrup, 1/4 cup organic unsweetened applesauce (instead of the full 1/2 cup maple syrup), and 1 cup unsweetened cashew milk. The muffins turned out great – they weren’t dry and had the right amount of sweetness from the blueberries and hint of maple syrup. In all reality, I couldn’t stop eating them. Lol. I omitted the frosting due to time but they still tasted good “plain.” Will definitely be making these again and next time try the frosting.
Nutritional info for the Blueberry breakfast cupcakes, please.
Hi Jackie! I don’t provide nutritional information at this time because everyone uses different brands of ingredients which often have differing nutritional values. I would recommend plugging the ingredients you used into a free online nutrition calculator like: http://www.myfitnesspal.com/recipe/calculator Hope this helps. Enjoy!
OMG! SO AMAZING. and not too difficult! I am terrible at baking and these were a dream! I topped them with lemon zest. Thank you!!! Fan favorite.
Yay Shelby! So happy to hear! Love the lemon zest addition. Yummy yum!
What are the calories in these?
Hi Ashley! I don’t provide nutritional information at this time because everyone uses different brands of ingredients which often have differing nutritional values. I would recommend plugging the ingredients you used into a free online nutrition calculator like: http://www.myfitnesspal.com/recipe/calculator Hope this helps. Enjoy!
Hello. I have just baked these but want to serve them Sunday breakfast. Can I freeze them ? Or better to leave them in an airtight tin?
Hi Pia! I apologize I’m just seeing your message. I recommend storing them at room temperature if enjoying within 2-3 days, in the refrigerator if planning to enjoy within 5 days of baking, and then in the freezer after that for up to 3 months. Let cool completely before storing. If storing in the refrigerator, place in a sealed container with a paper towel to absorb excess moisture. If storing in the freezer, place each muffin in individual plastic bags. Hope this helps. Enjoy!
The best muffins we ever made.
I just baked these and I am not a baker, omg they are so good. Thank you so much!!!!!!
[…] up on my list are these Healthy Whole Wheat Blueberry Cupcakes and Banana Breakfast Cookies. I love having baked treats like these tucked into the freezer for […]
Guilt-less cupcakes that I can eat for breakfast? YES PLEASE! These look incredible!!!
Thanks Bethany! Delicious and nutritious, what more could you ask for?! 🙂
YES! I’ve been looking for a healthy blueberry muffin recipe and this looks perfect! Last time I tried blueberry muffins they turned out too sour – I think because of the berries but I’m not sure? Hopefully these will turn out better, I’m excited to make them now!! Also I follow you on instagram and I wanted to say your kids are sooooo adorable! Also I was wondering if you could direct me to a website where I can convert the ingredients to grams (i’m from england) because whenever I try and google a converter I get really different answers – thank you!
Hi Aliyah! Thanks so much for your sweet comments 🙂 I hope you love the breakfast cupcakes as much as we do! Here’s an online convertor that I’ve used and had success with: http://dish.allrecipes.com/cup-to-gram-conversions/ Hope this helps. Enjoy!