Pumpkin Swirl Cheesecake Yogurt Cupcakes Recipe

These pumpkin swirl cheesecake cups are a lighter take on classic pumpkin cheesecake, using Greek yogurt to keep the texture creamy and topping each cup with a swirl of pumpkin butter for Autumn flavor.

Pumpkin Swirl Cheesecake Yogurt Cupcakes

Fall is one of the best times for baking: cool weather, cozy sweaters, and the comforting spices of pumpkin and cinnamon. This recipe highlights those flavors while keeping the dessert lighter by using reduced-fat cream cheese and fat-free vanilla Greek yogurt. The pumpkin swirl on top adds color and an extra hit of pumpkin spice without overpowering the cheesecake base.

More Pumpkin Desserts you might enjoy:

• Pumpkin Roll Sponge Cake
• Pumpkin Cream Cheese Muffins
• No Bake Pumpkin Cheesecake
• Pumpkin Butterscotch Bars
• Pumpkin Hazelnut White Chocolate Biscotti

Recipe: Pumpkin Swirl Cheesecake Yogurt Cupcakes

Ingredients

• 12 reduced-fat vanilla wafers
• 8 oz reduced-fat cream cheese (1/3 less fat), softened
• 1/4 cup granulated sugar
• 1 tsp vanilla extract
• 6 oz fat-free vanilla Greek yogurt (such as Chobani or similar)
• 2 large egg whites
• 1 tbsp all-purpose flour
• 3/4 cup pumpkin butter or pumpkin pie filling

Instructions

1. Preheat the oven to 350°F (175°C). Line a standard 12-cup muffin tin with paper liners.
2. Place one vanilla wafer in the bottom of each liner to form the crust.
3. In a mixing bowl, beat the softened cream cheese with the sugar and vanilla until smooth. Use an electric mixer on low to medium speed to avoid overbeating.
4. Gradually add the Greek yogurt, then beat in the egg whites and flour just until combined. The mixture should be smooth but do not overwork it.
5. Spoon the cheesecake filling into the lined cups, filling each about halfway.
6. Place about 1 tablespoon of pumpkin butter on top of each filled cup. Use a toothpick or the tip of a knife to gently swirl the pumpkin butter into the cream cheese filling to create a marbled effect.
7. Bake for about 25 minutes, or until the centers are almost set—there should still be a slight jiggle but not liquid. Be careful not to overbake to keep the texture creamy.
8. Remove from the oven and cool to room temperature, then refrigerate for a few hours to fully set before serving. Chilling helps the flavors meld and makes slicing or handling easier.

Nutrition (per serving)

Calories: 117 kcal; Carbohydrates: 16 g; Protein: 4 g; Fat: 5 g; Fiber: 0.5 g; Sugar: 12.5 g; Cholesterol: small amount; Sodium: 24 mg

Tips and Variations

• Pumpkin Butter: Use either homemade pumpkin butter for a richer, spiced flavor or a good-quality commercial jar for convenience.
• Crust Options: If you prefer, swap vanilla wafers for graham cracker crumbs, crushed gingersnaps, or a nut-based crust to add texture and complementary flavors.
• Flavor Boost: Add 1/2 to 1 teaspoon of pumpkin pie spice or a pinch of cinnamon and nutmeg to the cheesecake filling for a warmer spice profile.
• Make-Ahead: These keep well chilled, making them a good make-ahead dessert. Chill for a few hours or overnight; remove from the fridge a short time before serving to take the chill off.
• Presentation: For an elegant finish, top each chilled cup with a small dollop of whipped cream and a light dusting of cinnamon just before serving.

Storage

Store the chilled cheesecake cups in an airtight container in the refrigerator. They stay best when properly chilled and are ideal for enjoying over the course of several days.

Final Note

This recipe delivers the classic creaminess of cheesecake with the seasonal lift of pumpkin and the tang of Greek yogurt, all in a convenient single-serve format. It’s a great option for holiday gatherings, potlucks, or whenever you want a small, satisfying pumpkin dessert without making a full-size cheesecake.