I create these muffins to combine the warm, cozy flavors of fall with a creamy cheesecake center, while using smarter ingredients so they feel indulgent without being heavy. They’re moist, fluffy, and packed with pumpkin spice — yet still enjoyable anytime. Healthy Pumpkin Cheesecake Muffins

Why You’ll Love This Recipe

I love how these muffins hit the sweet spot between comfort and nourishment. The pumpkin purée brings that rich autumn flavor, Greek yogurt (or a higher-protein substitute) gives tenderness and boosts texture, and the cheesecake swirl adds the decadent feel of dessert. When I bake these, I know I’m treating myself while also keeping things a little lighter and satisfying.

Ingredients

(Tip: You’ll find the full list of Ingredients and measurements in the recipe card below.)

For the Muffins:

200 g pumpkin purée
100 g Greek yogurt (vanilla or plain, at room temperature)
1 large egg (room temperature)
80-100 ml light milk (or plant-milk) + a dash of lemon juice (to mimic buttermilk)
1 teaspoon vanilla extract
100 g granulated sweetener (or normal/brown sugar/monkfruit, your choice)
150 g all-purpose flour (or a substitute such as oat flour or gluten-free flour)
60 g vanilla protein powder (optional; if using, reduce flour accordingly)
2-3 teaspoons cinnamon or pumpkin spice
1½ teaspoons baking powder
½ teaspoon baking soda
¼ teaspoon salt

For the Cheesecake Swirl:

80 g light cream cheese (or regular cream cheese if preferred)
2-3 tablespoons icing sugar (or monkfruit icing sugar for lower calories)
¼ teaspoon baking powder
½ teaspoon vanilla extract

Directions

Preheat the oven to 220 °C and line 8 muffin cups with liners.
In a bowl, combine the egg, pumpkin purée, Greek yogurt, sweetener, vanilla extract, and the milk + lemon juice “buttermilk” mix until smooth.
In another bowl, sift together the flour, protein powder (if using), baking powder, baking soda, salt, and the cinnamon/pumpkin spice.
Gently fold the dry ingredients into the wet mixture until just combined — avoid over-mixing so the muffins remain tender.
In a separate small bowl, beat together the light cream cheese, icing sugar, baking powder, and vanilla until smooth and lump-free.
Divide the muffin batter evenly among the 8 lined cups (fill about ¾ full). Then add dollops of the cheesecake mixture into the center of each muffin, and swirl slightly on top.
Bake at 220 °C for about 5 minutes, then reduce the oven to 180 °C and continue baking for about 20-25 minutes, or until a toothpick inserted into the muffin (not the cheesecake center) comes out clean or with just a few moist crumbs.
Let the muffins cool in the tin for 10-15 minutes, then transfer to a wire rack to cool fully. The cheesecake center will firm up as they cool.

Servings And Timing

Makes: 8 muffins
Prep time: About 10 minutes
Bake time: Approximately 20-25 minutes (plus the initial 5-minute high temperature step)
Total time: Roughly 30-35 minutes

Variations

Skip the protein powder and replace it with additional flour (about the same weight) if you prefer no added protein powder.
Use oat flour or a gluten-free 1:1 flour blend instead of all-purpose flour to make the muffins gluten-free.
Swap granulated sweetener for brown sugar or regular granulated sugar if you don’t need the low-calorie version.
Add a pinch of nutmeg or ginger alongside the cinnamon for extra warming spice.
For the cheesecake swirl, add some lemon zest for a tangy twist.
Make mini muffins instead of full size: shorten the baking time by a few minutes and watch closely.

Storage/Reheating

Refrigerator: Once the muffins are fully cooled, store them in an airtight container in the refrigerator for up to 3-5 days.
Freezer: Wrap each muffin individually in plastic wrap or foil, then place them in a freezer-safe bag and freeze for up to 3 months. To enjoy, thaw at room temperature or gently warm in the oven or microwave.
Reheating: For the best texture, reheat in a preheated oven at around 160 °C for about 5-8 minutes, or microwave for 20-30 seconds depending on your appliance. The cheesecake center will soften pleasantly when warmed.

FAQs

How can I replace the protein powder if I don’t have any?

If I don’t have protein powder, I simply omit it and replace it with an equivalent weight of regular flour. Then I might reduce the milk slightly because the flour absorbs more moisture than protein powder.

Can I use canned pumpkin pie filling instead of plain pumpkin purée?

I advise using plain pumpkin purée rather than pumpkin pie filling, because pie filling often contains added sugar, spices, and other ingredients that will alter the sweetness and texture of the muffins.

Why did the cheesecake center sink or collapse in some muffins?

A cheesecake center can sink if the batter is overmixed (which weakens structure), the muffins are removed too soon from the oven, or the cheesecake layer is too heavy compared to the muffin batter. Allowing the muffins to cool in the tin for 10-15 minutes helps the center set properly.

Can I make these muffins dairy-free?

Yes — I can swap the Greek yogurt for a plant-based yogurt (e.g., almond or coconut-based) and substitute the light cream cheese with a dairy-free cream cheese alternative. Texture and flavor may be slightly different, but they still turn out tasty.

Will the muffins keep their high-protein content if I make substitutions?

If I alter key ingredients — such as removing the protein powder or using lower-protein substitutes — then yes, the protein content will drop accordingly. The original version is designed to provide a higher protein amount per muffin.

Conclusion

I really enjoy how these muffins deliver the cozy flavors of pumpkin spice and creamy cheesecake in a lighter, fitter format. Whether I bake them for breakfast, a snack between workouts, or a comforting dessert, they hit the spot. If you love the flavor of pumpkin and the texture of cheesecake, these muffins are definitely worth baking — I hope you enjoy them as much as I do!