Pumpkin Cupcakes with Chocolate Ganache and Spiced Cream Cheese Frosting

Published October 23, 2011. Updated October 17, 2023

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Try this sophisticated spin on a fall treat with my pumpkin cupcakes with chocolate ganache and spiced cream cheese frosting! A plain cream cheese frosting will never do again.

Pumpking cupcakes with chocolate ganache and spiced cream cheese frostingSo, do I have you drooling yet? Simply put, these are by far the best fall cupcakes! There are countless pumpkin cupcake recipes everywhere you look, but they’re all pretty basic and just slightly lacking. Don’t get me wrong—I do love the traditional pumpkin cream cheese cupcake—but I think it’s time to fancy things up a bit. Hence, I developed this ultimate fall cupcake: the light fluffy moist pumpkin cupcake, smothered in thick chocolate ganache, piped with creamy spiced cream cheese frosting, and sprinkled with crunchy pecans.

There you have it! This pumpkin cupcake with chocolate ganache and spiced cream cheese frosting is officially fall’s best cupcake! Please do not attempt to throw in a different cupcake recipe in place of this one. TRUST ME. It is so light and delicate, so if you were expecting one of those heavy dense pumpkin cupcakes in its place… things just wouldn’t be the same. If you are looking to impress friends, colleagues, a loved one, your grandma =), and even yourself—try these cupcakes! You will not be disappointed. I fell in love with just one bite! They will leave you speechless and convince everyone you are a master chef.


Pumpkin cupcake with chocolate ganache and spiced cream cheese frosting with pumpkins in the background

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5 from 2 votes

Pumpkin Cupcakes with Chocolate Ganache and Spiced Cream Cheese Frosting

Soft and fluffy pumpkin cupcakes finished with rich chocolate and sweet tangy cream cheese frosting.
Servings: 24
Prep40 minutes
Cook20 minutes
Ready in: 1 hour


Thick Chocolate Ganache

Spiced Cream Cheese Frosting


  • Preheat oven to 350degrees. In a large mixing bowl whisk together flour, baking powder, baking soda, cinnamon, nutmeg, ginger, and salt, set aside. In a separate large mixing bowl, using an electric mixer, combine vegetable oil, applesauce, granulated sugar, brown sugar and vanilla. Add eggs and stir until combine. Stir in pumpkin puree and buttermilk and stir until well combine. Slowly add dry ingredients. Stir until no longer lumpy about 1 - 2 minutes. Pour about 1/4 cup mixture into buttered muffin cups or paper lined muffin cups and bake 20 - 23 minutes until toothpick inserted in center comes out clean. Let muffins cool 5 minutes in muffin tin. Remove to a wire rack and let cool 30 minutes.

Thick Chocolate Ganache

  • Place chocolate chips in a medium mixing bowl, set aside. In a small saucepan over medium heat, bring whipping cream just to a boil. Pour hot cream over chocolate chips and whisk until smooth. Spoon 1 tsp ganache over each cooled cupcake and spread near edges, allow to cool. Meanwhile make spiced cream cheese frosting.

Spiced Cream Cheese Frosting

  • In a large mixing bowl, with an electric mixer, whip together cream cheese and butter until fluffy. Add vanilla, salt, powdered sugar, cinnamon and nutmeg and whip until smooth and fluffy. Pipe cream cheese frosting over cooled chocolate ganache covered cupcakes and sprinkle cupcakes with chopped pecans.
Delicious pumpkin cupcakes with chocolate ganache

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  • Kap

    This cupcake is very moist and delicious. The chocolate ganache is easy and does not make the cupcake too sweet. I will make this again. I have already been asked for a copy of this recipe!

  • Harriet

    Baked these a few days ago, with freshly puréed pumpkin and apple sauce. They turn out great. Thank you.

    • Jaclyn

      Jaclyn Bell

      The fresh pumpkin and apple sauce sounds delicious! Glad you enjoyed these cupcakes Harriet, thanks for your review!

  • Chris

    Hi, Jaclyn. If I wanted to put some chocolate in the cupcake itself, what would you recommend? I’m not a very experienced baker….

  • Pumpkin lover

    Hey, Jaclyn, here to ask you again. How sweet is this recipe? Would it be a good combo to pop an oreo in this and remove the chocolate ganache? I’m also making pumpkin cupcakes with oreos hopefully! I love the idea of the spiced cream cheese frosting-yum!

  • Kadela

    Hi…i made these tonight but instead of store bought pumpkin puree i grated pumpkin on the finest side of the grater….and for some reason my frosting was runny, so i cudnt make a swirl as in the pic. Yes i followed the recipe to a T…help? wat cud’ve gone wrong?

    • Jaclyn

      Jaclyn Bell

      It could be the type of cream cheese (I prefer Philadelphia as it seems to be the smoothest) and also it may have been too soft, when it was softened you don’t want it to melt. You can whip it cold (the cream cheese) until fluffy then mix in the rest and you could cut back on the amount of cream cheese by a few ounces and that may help.

  • Caroline

    Just fell in love with this recipe so im gonna do this cupcakes but have some issues, i mean what is buttermilk? Well ive never seen buttermilk in my country. Is this just butter with milk? Or what?
    And applesauce is any other product i can use to replace apesauce?

    • Jaclyn

      Jaclyn Bell

      For the buttermilk, you can make a simple substitute by whisking together 1 cup minus 1 Tbsp milk with 1 Tbsp white vinegar or lemon juice and let it rest 3 minutes. For the applesauce if you can’t find it you can make that homemade here is a link (I might leave out the sugar though since I used unsweetened applesauce): http://www.simplyrecipes.com/recipes/applesauce/

  • Lauren Steen

    Made these last night and they were a hit! Best cupcakes for the fall! Thank you!

    • Jaclyn

      Jaclyn Bell

      I’m so glad you liked these Lauren! These are one of my favorite fall cupcakes too :)!