Delicious & Healthy Whole Wheat Pumpkin Spice Cake with Lighter Greek Yogurt Cream Cheese Frosting
Indulge in the perfect fall dessert with our incredibly soft and fluffy whole wheat pumpkin cake! Infused with a harmonious blend of the best pumpkin spices and crowned with our signature lighter Greek yogurt cream cheese frosting, this cake is an absolute dream for any autumn gathering or cozy evening in. It’s a delightful treat that proves healthy can be utterly delicious and satisfying.

As the leaves change and the air turns crisp, there’s nothing quite like the comforting aroma of pumpkin spice filling your kitchen. This season, I simply couldn’t resist creating one more decadent delight, perfect for pairing with my all-time favorite frosting. If you’ve been following Food Doodles for a while, you’ve probably noticed my deep affection for pumpkin recipes, especially pumpkin muffins. From classic pumpkin muffins to these incredibly healthy chocolate chip pumpkin muffins, pumpkin is a staple in my fall baking. So, it was only a matter of time before I channeled that love into creating the ultimate pumpkin cake.
This particular whole wheat pumpkin cake recipe is a loving adaptation of my go-to pumpkin muffin recipe. To elevate it from a muffin to a truly luxurious cake experience, I made a few strategic tweaks. I slightly increased both the sugar and the pumpkin puree content, resulting in a cake that is exceptionally moister and even more flavorful than its muffin counterpart. The goal was to achieve that rich, tender crumb that defines a perfect cake, and I’m thrilled with the outcome.
While I adore this Greek yogurt cream cheese frosting, it’s worth noting that this versatile cake base could be enjoyed in many ways. Imagine baking it as a loaf, then perhaps drizzling it with a simple, sweet glaze instead of a full frosting. The possibilities are truly endless, making this recipe a fantastic addition to your baking repertoire.
Why You’ll Love This Healthy Whole Wheat Pumpkin Cake
Deceptively Healthy & Utterly Delicious
One of the best features of this whole wheat pumpkin cake is that it doesn’t taste “healthy.” The robust and aromatic pumpkin spices—cinnamon, ginger, cloves, and nutmeg—work their magic, completely masking any perceived “whole wheat” flavor. What you get is a rich, traditional-tasting pumpkin cake that happens to be made with whole grains. This makes it a fantastic choice for those looking to incorporate more fiber into their diet without sacrificing taste or texture.
For those who might be skeptical about baking with whole wheat flour, I highly recommend giving white whole wheat flour a try. It offers all the nutritional benefits of traditional whole wheat flour but has a lighter color and milder flavor, making it an excellent substitute in many baking recipes, especially cakes and muffins. This specific flour ensures your cake remains wonderfully soft and airy, a hallmark of a truly great dessert.
The Magic of Greek Yogurt Cream Cheese Frosting
The frosting is where this cake truly shines with a lighter touch. My favorite Greek yogurt cream cheese frosting provides a delightful tang and creamy texture without being overly heavy or sweet. Traditional cream cheese frostings can sometimes be quite rich, but by incorporating Greek yogurt, we achieve a luscious frosting that complements the pumpkin cake beautifully, adding a refreshing note and a boost of protein. It’s the perfect balance to the warm spices of the cake, creating a dessert that feels indulgent yet surprisingly light.
The combination of cream cheese, Greek yogurt, honey, vanilla, and a hint of lemon juice creates a frosting that is both bright and comforting. It spreads smoothly and holds its shape, making your cake look as good as it tastes. This frosting is a game-changer for anyone who loves cream cheese frosting but desires a less guilt-inducing option.
Baking Tips for a Perfect Pumpkin Spice Cake
Ingredient Quality Matters
Using high-quality ingredients will always yield the best results. For the pumpkin puree, make sure it’s 100% pure pumpkin, not pumpkin pie filling, which contains added sugars and spices. Freshly ground spices will also make a noticeable difference, intensifying the fall flavors. As for the butter, ensure it’s properly softened to cream smoothly with the sugar, creating an airy base for your cake batter.
Don’t Overmix Your Batter
One of the golden rules of baking, especially with whole wheat flour, is to avoid overmixing. Once you add the dry ingredients to the wet, mix just until everything is combined and no streaks of flour remain. Overmixing can develop the gluten in the flour too much, leading to a tough or dense cake. A light hand will ensure your pumpkin cake stays perfectly soft and fluffy.
Achieving the Perfect Moisture
Pumpkin is naturally very moist, and this recipe leverages that. The increased pumpkin puree content, along with the right balance of sugar and fats, ensures a beautifully tender crumb. When checking for doneness, rely on the toothpick test: insert a toothpick into the center of the cake; if it comes out clean or with just a few moist crumbs, your cake is ready. Overbaking can dry out the cake, so keep a close eye on it during the last few minutes.
Cooling is Crucial
It can be tempting to frost a cake as soon as it comes out of the oven, but patience is key! Allow the cake to cool completely in the pan on a wire rack before attempting to frost it. A warm cake will melt your beautiful Greek yogurt cream cheese frosting, leading to a messy rather than magnificent dessert. This cooling period also allows the cake’s structure to set, making it easier to handle and cut.
I was also thinking, this whole wheat pumpkin cake could be an excellent last-minute dessert for tonight in place of pie, if you don’t have anything else planned yet. Its ease of preparation and comforting flavors make it a delightful alternative that everyone will enjoy.
Variations and Serving Ideas
Beyond the Frosting: Glazes and Toppings
While the Greek yogurt cream cheese frosting is fantastic, this cake is incredibly versatile. If you’re looking for an alternative, consider a spiced glaze! A simple powdered sugar glaze infused with extra cinnamon, nutmeg, or a hint of ginger would be absolutely divine. This lighter option would still provide a lovely sweetness and enhance the cake’s autumnal flavor profile. For an extra touch of elegance and crunch, sprinkle some chopped pecans or walnuts over the glaze or directly onto the frosting. The nutty flavor and texture would complement the pumpkin beautifully.
For those who love a bit of crunch, consider adding a streusel topping before baking. A simple mix of flour, brown sugar, butter, and a dash of cinnamon would create a delightful crispy layer. Another idea is to fold in some chocolate chips or dried cranberries into the batter for added bursts of flavor and texture. This cake is truly a blank canvas for your creative baking ideas!
Serving Suggestions for Any Occasion
This Whole Wheat Pumpkin Spice Cake is perfect for almost any occasion. It makes a fantastic dessert for Thanksgiving or other fall holidays, offering a slightly lighter alternative to traditional heavy pies. It’s also simple enough for an everyday treat, perfect with a cup of coffee or tea on a chilly afternoon. You can serve it as individual slices, or even in smaller portions for a delightful mini-dessert spread.
Don’t forget about these crustless pumpkin pie bars for another super quick and easy pumpkin treat that will satisfy your fall cravings. We always have time for another pumpkin recipe, right? I know I’m definitely not getting sick of pumpkin anytime soon!

Whole Wheat Pumpkin Spice Cake with Greek Yogurt Cream Cheese Frosting
Ingredients
- 1 1/2 cups (187g) white whole wheat flour
- 1/2 teaspoon baking powder
- 1/4 teaspoon baking soda
- 2 teaspoon cinnamon
- 3/4 teaspoon ground ginger
- 3/4 teaspoon cloves
- 3/4 teaspoon nutmeg
- 1/2 teaspoon sea salt
- 1/2 cup salted butter softened
- 1 cup coconut sugar or brown sugar
- 2 large eggs
- 1 teaspoon vanilla
- 1 cup pumpkin puree
- Pecans to top if desired
Instructions
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Preheat oven to 350 degrees F (175 C). Prepare an 8×8 inch or 9×9 inch baking pan by lining it with parchment paper or by lightly greasing the sides and bottom. Set aside.
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In a medium bowl, whisk together the white whole wheat flour, baking powder, baking soda, cinnamon, ground ginger, cloves, nutmeg, and sea salt. Ensure all dry ingredients are well combined. Set aside.
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In a large mixing bowl or stand mixer, beat the softened salted butter until it is light and fluffy. Gradually add the coconut sugar (or brown sugar) and continue to beat until the mixture is well combined and has a fluffy texture.
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Add the large eggs one at a time, beating well after each addition until fully incorporated. Stir in the vanilla extract and pumpkin puree until the mixture is smooth and evenly combined.
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Gradually add the reserved dry ingredients to the wet ingredients. Mix on low speed or by hand, just until all the dry ingredients have been incorporated and the batter is smooth. Be careful not to overmix.
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Pour the cake batter into the prepared pan and smooth the top with a spatula. Place in the preheated oven and bake for 35-40 minutes, or until a wooden toothpick inserted into the center of the cake comes out clean. Remove the cake from the oven and let it cool completely on a wire rack before applying the frosting.

Greek Yogurt Cream Cheese Frosting
Ingredients
- 3 oz cream cheese
- 1/4 C plain Greek yogurt
- 1/2 tsp vanilla
- 2 1/2 tbsp honey
- 1/2 tbsp lemon juice
Instructions
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Combine the softened cream cheese, plain Greek yogurt, vanilla extract, honey, and lemon juice in a food processor or with an electric mixer. Process or beat until the mixture is completely smooth and creamy. Transfer to an airtight container and keep refrigerated until ready to use. This frosting is best when chilled for at least 30 minutes before spreading.

I hope you love this Whole Wheat Pumpkin Spice Cake as much as I do. It’s a truly delightful dessert that brings all the warmth and comfort of autumn into your home, with a wholesome twist. Enjoy every soft, spiced bite!