Pumpkin Cupcakes with Chocolate Filling and Pumpkin Cream Cheese Icing


Pumpkin Cupcakes with Chocolate Filling and Cream Cheese Icing

I had the idea for these cupcakes over a year ago, and now I am wondering why it took me so long to make them. They were so very good! I normally try to keep my recipe names short, but this time there was really no way to shorten it without losing one of the things that makes these so great.

It all started on a drive to Asheville last year. It was the middle of fall and we were driving through the Smokies at just about the peak of fall color. The leaves were vivid shades of red, orange, and yellow and it was just gorgeous. So naturally, I was thinking of food. And not just any food – pumpkin treats. I had recently made pumpkin cookies with chocolate chips and had come to the same conclusion I often do with pumpkin/chocolate recipes: there was simply too much chocolate and it overpowered the pumpkin flavors. In fact, I make this great Harvest Cake that is chocolate with pumpkin cream cheese filling, covered in chocolate ganache. Yes, it is delicious, but I am always left wanting more pumpkin. So I started to think, what if I just made it pumpkin cake instead of chocolate? Would the ganache still be too much?

Then I had a brilliant flash. What if I made cupcakes, filled them with chocolate ganache, and used the pumpkin cream cheese filling as icing? I suspected this would be the perfect ratio of pumpkin and chocolate. Then I sat on the idea for a year. Last weekend, I finally decided it was now or never ,and I am so glad I finally made these! The ratio is perfect! Lots of great pumpkin flavor in both the cake and the icing, and just enough chocolate to make the perfect bite. Mmmm.

Pumpkin Cupcakes with Chocolate Filling SQ

To create this perfect combo, I first made the The Brown Eyed Baker’s Pumpkin Cupcakes, which are simple and delicious.¬†Once they were cool, I used a technique for filling cupcakes that I learned from a Baking Bites recipe for Vampire Cupcakes (which are also awesome for Halloween). You use a paring knife held at an angle to cut what is essentially a cone of cake out of the top of each cupcake, cut off the pointy end, fill the cupcake, and add the little cap back on top. The blog has a great tutorial and even a video if you need more guidance. Plus you get to eat the little extra bits of cake that you cut out to make room for filling! I then made the ganache and pumpkin cream cheese filling from my Harvest Cake and used the filling as icing. I am really bad at making icing look all fancy, so just pretend these are prettier. I guarantee that they taste good enough to make up for it!

Note that these do take some time, but not a ton. I made the cupcakes one evening and filled and frosted them the next night. But you could do this in one day if you made the cupcakes early enough. You just need time for them to cool. The filling step is really not that labor-intensive, as you can prep the cupcakes while waiting for the ganache to firm up a bit. These would be great for any fall party or a welcome addition to the Thanksgiving dessert line-up!

Pumpkin Cupcakes with Chocolate Filling and Pumpkin Cream Cheese Icing

Yield: 12 cupcakes


  • For the Cupcakes:
  • 1 1/3 cup flour
  • 1 tsp. baking powder
  • 1 tsp. baking soda
  • 1/2 tsp. salt
  • 1/2 tsp. cinnamon
  • Pinch each of nutmeg and cloves
  • 3/4 cup canned pumpkin
  • 1/2 cup sugar
  • 1/2 cup brown sugar
  • 1/2 cup vegetable oil
  • 2 eggs
  • For the Ganache:
  • 1/2 cup heavy cream
  • 4 oz semisweet chocolate
  • For the Pumpkin Cream Cheese Icing:
  • 8 oz cream cheese, softened
  • 1/3 cup canned pumpkin
  • 1/4 cup sugar
  • 1/2 tsp. cinnamon


  1. Preheat oven to 350 F. Prep a 12-cup muffin pan with liners.
  2. In a medium bowl, combine the flour, baking powder, baking soda, salt, cinnamon, nutmeg and cloves and whisk to combine.
  3. In a large bowl, stir the pumpkin, sugar, brown sugar, and vegetable oil together till well combined. Then whisk in the eggs, one at a time.
  4. Fold in the flour mixture in a couple additions till the batter is uniform, but don't overmix. Divide the batter among the prepared muffin cups, filling each about 3/4 full.
  5. Bake at 350 F for 18-20 minutes, until a toothpick inserted in the middle comes out clean. Cool completely.
  6. Make the ganache by bringing the heavy cream just to boiling in a small saucepan. Remove from heat and add the chocolate. DO NOT STIR. Let it sit for 5 minutes. Then stir till smooth.
  7. Set the ganache aside to cool for about 20 minutes. You want it to thicken up quite a bit before you fill the cupcakes.
  8. While waiting for it to thicken, prep the cupcakes by cutting a cone out of the top of each one. Cut the tip off each cupcake cone and set the little cupcake lid aside. Be sure to keep the cupcake lid with the corresponding cupcake so that they fit back together later.
  9. Once the ganache has thickened a bit, spoon a couple tablespoons into the well in each cupcake. Then add the little cupcake lid back on top. Repeat until all cupcakes are filled. You will have ganache left over.
  10. To make the icing, beat the cream cheese, pumpkin, sugar, and cinnamon together until well combined and fluffy. The mixture is a bit thicker than regular icing. Frost each cupcake.
  11. If not served right away, store covered in the fridge. Set out at room temperature for about 15 minutes before serving.