These pumpkin cupcakes with cream cheese filling are soft, moist, and full of warm pumpkin spice flavor, with a creamy cheesecake-like center baked right inside. They’re finished with a light whipped cream cheese frosting that’s less rich than traditional buttercream.
Made with pumpkin puree, brown sugar, and warm spices, these filled pumpkin cupcakes are a lovely fall dessert for Halloween, Thanksgiving, or whenever you’re in the mood for something pumpkin.
If you know me by now, you know I love adding cream cheese fillings to just about anything, sweet or savory. And these pumpkin cupcakes are another excuse to do just that.
I used my favorite pumpkin cupcake batter, added a simple filling of cream cheese, sugar, and vanilla, and baked everything together. You get a soft pumpkin cupcake with a creamy surprise in the center.
For the topping, I wanted something lighter than my usual cream cheese frosting, so I whipped cream and stabilized it with cream cheese. It holds its shape beautifully without being too heavy.
Why You’ll Love These Cupcakes
- Creamy surprise inside – A simple cream cheese filling bakes right into the center of each cupcake.
- Soft and moist – Pumpkin puree, brown sugar, and oil give the cupcakes a tender crumb.
- Light whipped frosting – Whipped cream stabilized with cream cheese makes a smooth, airy topping.
- Perfect for fall – Pumpkin, cinnamon, and warm spices make these lovely for autumn gatherings.
Ingredients and Substitutions
- For the pumpkin cupcakes
- All-purpose flour – Gives the cupcakes structure while keeping the crumb tender. Measure by weight for the best results.
- Baking powder and baking soda – Help the cupcakes rise and stay light.
- Salt – Balances the sweetness and brings out the pumpkin spice flavor.
- Pumpkin spice and cinnamon – Add warm fall flavor. You can use homemade or store-bought pumpkin spice.
- Light brown sugar – Adds sweetness, moisture, and a subtle caramel flavor.
- Neutral oil – Keeps the cupcakes soft and moist, even after refrigeration.
- Eggs – Provide structure and help bind the batter.
- Pumpkin puree – Use plain pumpkin puree, not pumpkin pie filling, which already contains sugar and spices.
- Vanilla extract – Rounds out the flavor.
- For the cream cheese filling
- Cream cheese – Use full-fat block-style cream cheese for a thick, creamy filling. Avoid whipped or spreadable varieties.
- Granulated sugar – Sweetens the filling without overpowering the tanginess of the cream cheese.
- Vanilla extract – Adds a little extra flavor.
- For the whipped cream cheese frosting
- Heavy whipping cream – Use cold cream with at least 35% fat so it whips properly.
- Cream cheese – Stabilizes the whipped cream and adds a slight tang.
- Powdered sugar – Sweetens the frosting and blends smoothly.
- Vanilla extract – Adds flavor.
How to Make Pumpkin Cupcakes with Cream Cheese Filling
Step 1 – Prepare the cream cheese filling
- Beat the cream cheese, sugar, and vanilla until smooth and creamy.
- Set aside while preparing the cupcake batter. Keep refrigerated if the kitchen is warm.
Step 2 – Make the pumpkin cupcake batter
- Preheat the oven to 350°F / 175°C. Line a 12-cup muffin pan with cupcake liners.
- In a bowl, whisk together the flour, baking powder, baking soda, salt, pumpkin spice, and cinnamon.
- In a separate bowl, whisk the brown sugar and oil until combined. Add the eggs and vanilla, then whisk until smooth.
- Stir in the pumpkin puree.
- Add the dry ingredients to the wet ingredients and mix just until combined. Do not overmix.
Step 3 – Fill and bake the cupcakes
- Spoon a little pumpkin batter into each cupcake liner.
- Add about a tablespoon of cream cheese filling to the center.
- Cover with the remaining pumpkin batter, making sure the cream cheese filling is enclosed.
- Bake for approximately 22–27 minutes, or until the pumpkin cake is set and a toothpick inserted into the cake portion comes out clean or with a few moist crumbs.
- Let the cupcakes cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.
Step 4 – Make the whipped cream cheese frosting
- Beat the cream cheese with the powdered sugar and vanilla until smooth.
- Gradually add the cold whipping cream while mixing on low speed.
- Increase to medium-high speed and whip until the frosting holds firm peaks. Stop as soon as it is thick enough to pipe.
- Transfer to a piping bag fitted with your favorite nozzle and pipe onto the completely cooled cupcakes.
Storage and Make Ahead
- Refrigerator – Because these cupcakes have a baked cream cheese filling and whipped cream cheese frosting, store them in an airtight container in the refrigerator for up to 4 days.
- Make ahead – Bake the cupcakes a day ahead and refrigerate once cooled. Prepare and pipe the whipped cream cheese frosting closer to serving for the freshest appearance.
- Freezing – The unfrosted cupcakes can be frozen for up to 2 months. Wrap them individually and store in a freezer-safe container. Thaw overnight in the refrigerator before frosting.
- Serving – For the best texture, let the cupcakes sit at room temperature for about 15–20 minutes before serving. Don’t leave the cream cheese cupcakes unrefrigerated for more than 2 hours.
Pumpkin Cupcakes with Cream Cheese Filling
These moist pumpkin cupcakes are soft, tender, and full of warm fall flavor from pumpkin puree, cinnamon, and pumpkin spice. Topped with a smooth, tangy cream cheese frosting, they’re an easy pumpkin dessert for fall baking, Halloween, Thanksgiving, or any autumn gathering.
Video
Ingredients
Cream Cheese Filling
- 170 g (6 oz) Cream Cheese full fat
- 3 tbsp Sugar
- ½ tsp Vanilla extract
Cupcakes
- 170 g (1⅓ cups) All-purpose flour
- 1¼ tsp Baking powder
- ¼ tsp Baking soda
- ¼ tsp Salt
- 1 tsp Pumpkin Spice
- 1 tsp Ground cinnamon
- 2 large Eggs large
- 225 g (1 cups) Sugar white or brown
- 75 ml (⅓ cup) Cooking oil
- 280 g (1 cups) Pumpkin puree
- 1 tsp Vanilla Extract
Cream cheese frosting
- 240 g (1 cup) Heavy cream room temperature
- 113 g (4 oz) Cream cheese softened
- 60 g (½ cup) Powdered sugar
- ¼ tsp Salt
- 1 tsp Vanilla extract
Method
- Cream cheese filling – Beat the cream cheese, sugar, and vanilla until smooth. Set aside.170 g Cream Cheese , 3 tbsp Sugar, ½ tsp Vanilla extract
Pumpkin Cupcakes
- Preheat the oven to 350°F / 175°C. Line a 12-cup cupcake pan.
- Dry ingredients – Whisk together the flour, baking powder, baking soda, salt, pumpkin spice, and cinnamon.170 g All-purpose flour, 1¼ tsp Baking powder, ¼ tsp Baking soda, ¼ tsp Salt, 1 tsp Pumpkin Spice, 1 tsp Ground cinnamon
- Batter – In another bowl, whisk the brown sugar, oil, eggs, and vanilla until combined. Stir in the pumpkin puree. Add the dry ingredients and mix just until combined.2 large Eggs, 225 g Sugar, 75 ml Cooking oil, 280 g Pumpkin puree, 1 tsp Vanilla Extract
- Assemble – Divide some batter among the cupcake liners. Add a spoonful of cream cheese filling to each, then cover with the remaining batter.
- Bake for approximately 22–24 minutes, checking that the cake is set. Cool completely.
Whipped cream cheese frosting
- Beat the cream cheese, powdered sugar, and vanilla until smooth. Gradually add the cold whipping cream, then whip until firm peaks form.240 g Heavy cream, 113 g Cream cheese, 60 g Powdered sugar, ¼ tsp Salt, 1 tsp Vanilla extract
- Pipe onto the cooled cupcakes and refrigerate until serving.
Notes
- Use plain pumpkin puree, not pumpkin pie filling.
- Keep the cream cheese filling centered and completely covered with batter.
- Avoid overmixing the cupcake batter.
- Check the cake around the filling for doneness, rather than inserting a toothpick directly through the cream cheese.
- Use cold heavy cream for the frosting and stop whipping once it holds firm peaks.
- Refrigerate frosted cupcakes in an airtight container for up to 4 days.
Equipment you will need
Nutrition
Tried this recipe?
Mention @veenaazmanov_kitchen or tag #veenaazmanovkitchen!Tips for Success
- Keep the filling centered. Cover the cream cheese completely with pumpkin batter so it doesn’t spread onto the cupcake edges.
- Don’t overfill the liners. The cream cheese adds volume, so divide the batter and filling evenly among the cupcakes.
- Use full-fat cream cheese. It gives the filling a creamier consistency and helps stabilize the whipped frosting.
- Don’t overmix the batter. Mix only until the flour disappears to keep the cupcakes tender.
- Check the cake, not the filling. A toothpick inserted through the cream cheese center may look moist even when the cupcakes are baked.
- Chill before frosting if necessary. Both the cupcakes and frosting should be cool before piping.
More cupcakes
- Chocolate Chip Pumpkin Cupcakes
- Pumpkin Cupcakes with Cream Cheese Frosting
- Soft Moist Honey Cupcakes with Honey Frosting
- Maple Cupcakes with Maple Frosting
- Caramel Cupcake Recipe
Troubleshooting
| Problem | Possible cause and solution |
|---|---|
| Cream cheese filling sinks | Some settling is normal. Use thick cream cheese and avoid making the filling too runny. |
| Filling spreads into the batter | Keep the filling in the center and cover it completely with pumpkin batter. |
| Cupcakes are dense | Too much flour or overmixing. Weigh the flour and mix gently. |
| Cupcakes sink after baking | They may be underbaked. Check that the cake surrounding the filling is fully set. |
| Whipped frosting is too soft | The cream may be too warm or underwhipped. Chill briefly, then whip carefully until firm. |
Frequently Asked Questions
Can I use canned pumpkin puree?
Yes. Plain canned pumpkin puree works perfectly. Avoid pumpkin pie filling, which contains added sugar and spices.
Can I make these without the cream cheese filling?
Absolutely. For the classic version, try my Pumpkin Cupcakes with Cream Cheese Frosting.
Can I use regular cream cheese frosting instead?
Yes. A traditional cream cheese frosting works well, although the whipped cream cheese version is lighter and less buttery.
Why did my cream cheese filling disappear into the cupcakes?
The filling may have been too soft or spread into the batter during baking. Use thick cream cheese, avoid overmixing the filling, and keep it centered.
Can I make these into muffins?
You can bake them without frosting for a muffin-style treat, but if you want a bakery-style version with a crumble topping, try my Pumpkin Cream Cheese Muffins with Crumble.
More cream cheese filled recipes
- Stuffed Brownie Cookies
- Pumpkin Cream Cheese Muffins (Starbucks Copycat)
- Cheese Stuffed Chicken Breast Recipe
- Cheesecake Cream Puffs Recipe
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Hi, I’m Veena
I’m the recipe developer, baker, and food photographer behind Veena Azmanov Kitchen.
I’ve spent years developing and testing recipes, from everyday meals and homemade breads to cakes and desserts.
I share the practical tips and little details I’ve learned along the way so you can get great results in your own kitchen.
