Irresistible Whole Wheat Applesauce Cupcakes with Light Greek Yogurt Cream Cheese Frosting
Soft, incredibly moist applesauce cupcakes crafted with wholesome 100% whole wheat flour – yet so delicious, you’d never guess! These perfectly spiced, buttery treats are crowned with the most delightful, lightened-up cream cheese frosting, made with a secret ingredient: Greek yogurt. Get ready to discover your new favorite fall dessert!

Prepare your taste buds for an extraordinary treat! These applesauce cupcakes are truly exceptional, offering a symphony of flavors and textures that will surprise and delight you. Achieving this level of perfection took a few careful attempts, but the resulting recipe is nothing short of ideal.
The star ingredient, applesauce, plays a pivotal role in creating these culinary masterpieces. It infuses the cupcakes with an unparalleled moisture, making each bite incredibly tender, and lends a bright, fruity essence that elevates the overall flavor profile. Coupled with a warming blend of spices, these applesauce cupcakes evoke the cozy, comforting spirit of autumn, making them the perfect indulgence for any crisp day.
The Secret to Healthier Indulgence: Whole Wheat Flour
One of the most remarkable aspects of these cupcakes is their use of 100% whole wheat flour. Many bakers shy away from whole wheat, fearing dense, dry, or overly earthy results. However, with the right technique and the choice of white whole wheat flour (which has a milder flavor and lighter texture than traditional whole wheat), you can achieve baked goods that are just as tender and flavorful as those made with all-purpose flour, but with added nutritional benefits.
Whole wheat flour retains the bran and germ of the wheat kernel, providing more fiber, protein, and essential nutrients compared to refined flours. In this recipe, the natural moisture from the applesauce works in perfect harmony with the whole wheat flour, ensuring a soft, fluffy texture that defies expectations. If you prefer, all-purpose flour can be used as a substitute, but we highly encourage you to give the whole wheat version a try – you might just become a convert!
Introducing the Irresistible Greek Yogurt Cream Cheese Frosting
And then there’s the frosting. Oh, the frosting! This isn’t just any cream cheese frosting; it’s a lighter, tangier version that I’ve been utterly obsessed with since I first used it on my whole wheat carrot cake. It’s a revelation, offering all the creamy indulgence of a classic cream cheese frosting but with a fresh, less heavy feel.
The inclusion of Greek yogurt not only significantly lightens the frosting but also introduces a delightful tang that beautifully complements the sweet, spiced applesauce cupcakes. Its texture is notably smoother and a touch thinner than a traditional cream cheese frosting, yet it holds its shape perfectly, without any running or dripping. This makes it an ideal choice for piping or spreading generously onto your cooled cupcakes.
Due to its fresh dairy content, this exquisite frosting should ideally be kept refrigerated. For the best experience, I recommend frosting your cupcakes just before serving. While storing frosted cupcakes in the fridge can sometimes make baked goods seem a bit drier than they actually are, these applesauce delights remain wonderfully moist even after chilling. In fact, I have some in the fridge right now, and they are still absolutely delicious!
The Importance of Precision: Why You Should Weigh Your Flour
You’ll notice a small but significant change in this recipe that I’m incredibly excited about – and, dare I say, a little embarrassed it took me so long to adopt: I’ve finally started using weight measurements for flour. For years, I, like many home bakers, relied solely on volume measurements (cups), but I’ve come to realize the profound impact of precision in baking.
While I will still provide cup measurements as I personally use them, if you frequently encounter inconsistencies or problems with your baked goods, there’s a 99% chance the culprit is inaccurate flour measurement. The variability when using measuring cups is astonishing; a cup of flour can easily differ by 20-30% in weight depending on how it’s scooped, sifted, or packed.
If you have a passion for baking, investing in a kitchen scale is one of the best decisions you can make. They are surprisingly inexpensive, incredibly precise, and immensely versatile – I use mine constantly for far more than just baking. This simple tool will revolutionize your baking accuracy, leading to consistently perfect results. I am actively working on revisiting and updating all my older recipes with precise weight measurements, ensuring they are 100% accurate for everyone to enjoy. In the meantime, savor every bite of these perfectly spiced applesauce cupcakes!
Tips for Baking Flawless Applesauce Cupcakes
- Room Temperature Ingredients: Ensure your butter and eggs are at room temperature. This helps them cream together more smoothly, creating a light, airy batter that contributes to a tender cupcake.
- Don’t Overmix: Once you add the dry ingredients to the wet, mix only until just combined. Overmixing develops gluten, which can lead to tough, dense cupcakes. A few lumps are perfectly fine!
- Applesauce Consistency Matters: The note in the recipe about applesauce quantity is crucial. If using a thinner, store-bought applesauce, measure slightly under 1 cup. If you have thicker homemade applesauce, a full cup will likely be perfect. The goal is to avoid an overly wet batter.
- Spice it Right: The blend of cinnamon, nutmeg, and cloves creates that iconic “fall” flavor. Feel free to adjust the amounts slightly to suit your preference, adding a pinch more if you love a bolder spice profile.
- Cool Completely: Always ensure your cupcakes are fully cooled before attempting to frost them. Warm cupcakes will melt the frosting, leading to a messy rather than a magnificent result.

Applesauce Cupcakes with Greek Yogurt Cream Cheese Frosting
Ingredients
- 1/2 cup salted butter softened
- 3/4 cup brown sugar packed
- 2 large eggs
- 2 teaspoons vanilla
- 1 cup applesauce scant
- 1 1/2 cups (187g) white whole wheat flour (or all-purpose flour)
- 1/4 teaspoon baking soda
- 1 1/2 teaspoon baking powder
- 1/2 teaspoon salt
- 2 teaspoons cinnamon
- 1/4 teaspoon nutmeg
- 1/4 teaspoon cloves
- 1 Recipe Greek Yogurt Cream Cheese Frosting recipe below
Instructions
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Preheat oven to 375 °F (190 °C) Prepare a muffin tin by lining with paper liners or lightly greasing with non stick spray.
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In a bowl beat the butter until soft and fluffy. Add the brown sugar and beat again until fluffy. Add the vanilla and eggs and beat in until combined, one at a time. Add in the applesauce and mix until just combined.
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In a small bowl stir together the flour, baking soda, baking powder, salt, cinnamon, nutmeg and cloves. Add the dry ingredients to the wet ingredients and beat just until combined.
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Divide evenly among the 12 muffin cups. Place in the oven and bake for 17-19 minutes until a toothpick comes out clean and cupcakes are beginning to turn golden.
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Remove from the oven and let cool in the muffin tin for 5 minutes before removing and placing on a cooling rack.
Notes

Greek Yogurt Cream Cheese Frosting
Ingredients
- 3 oz cream cheese
- 1/4 cup plain Greek yogurt
- 1 teaspoon vanilla
- 1/2 tablespoon lemon juice
- 2 1/2 tablespoons honey
Instructions
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With a hand blender whip the cream cheese until soft. Add all the other ingredients and beat until smooth.
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With a food processor simply add all the ingredients and blend until smooth.
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Frost cupcakes or cake just before serving as this frosting should be kept in the fridge.
Serving & Storage Recommendations
To ensure your applesauce cupcakes remain at their peak deliciousness, I recommend storing any unfrosted cupcakes in an airtight container at room temperature for up to 2-3 days. If they are frosted with the Greek yogurt cream cheese frosting, they should be stored in the refrigerator due to the fresh dairy components. Place them in an airtight container in the fridge for up to 3-4 days. For the best flavor and texture, allow refrigerated cupcakes to come to room temperature for about 15-20 minutes before serving.
These versatile cupcakes are perfect for any occasion, from a casual family treat to a festive gathering. You can also experiment with toppings like a sprinkle of extra cinnamon, a dusting of powdered sugar, or even some finely chopped walnuts or pecans for added crunch.
Embrace the Flavors of Fall
These Whole Wheat Applesauce Cupcakes with Greek Yogurt Cream Cheese Frosting are more than just a dessert; they are a celebration of comforting flavors and wholesome ingredients. They prove that healthy baking doesn’t mean sacrificing taste or indulgence. The perfect balance of sweet apples, warm spices, and a light, tangy frosting makes these cupcakes an absolute must-try. Whether you’re looking for a delightful treat for yourself, a delicious offering for friends, or simply craving the taste of autumn, this recipe delivers every time. Enjoy the process of baking them, and even more so, enjoy devouring these incredible homemade delights!