Pumpkin Cupcakes with Whipped Ganache Frosting

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Perfectly pumpkin-spiced and moist Pumpkin Cupcakes with Whipped Ganache Frosting are an easy small batch cupcake recipe.  The cupcakes are infused with plenty of pumpkin and cozy spices and topped with a whipped ganache and whipped cream cheese frosting.  A must-have dessert for your holiday menu!

POST UPDATED November 2021

Small Batch Pumpkin Cupcakes

I’ve made a few small batches of cupcakes, and I have to say that this is one recipe where I wanted more.  It could be the cool Fall air and anticipation for the holidays.  Or it could be that they were just that good.

Sometimes with pumpkin recipes, you can lose the flavor of the pumpkin.  Especially in baking – unless you are making a straight-up pumpkin pie.  However, this small batch of Pumpkin Cupcakes is full of pumpkin and spice.

What You Can Expect With These Pumpkin Cupcakes

  • Moist – The pumpkin and brown sugar in these cupcakes will help keep them moist.
  • Easy – Let’s be honest – with a small batch recipe for 4 cupcakes, it’s hard not to make an easy batch of cupcakes! 
  • Pure Pumpkin Flavor – Pure canned pumpkin is the star of these cupcakes.  And to be clear, it is pure pumpkin, and not pumpkin pie filling!
  • Cozy Spices – We make sure to cover all the Fall spices in this small batch cupcake recipe.  Cinnamon, Ginger, Nutmeg, and Cloves – or better known as Pumpkin Pie Spice!
  • Variety of Frosting – For this recipe, I made two frostings to add complimentary layers of flavor to the Pumpkin Cupcakes.  Whipped Chocolate Ganache and Whipped Cream Cheese Frosting add a rich and tangy bite, and because they are both whipped, it keeps the cupcakes light!
Pumpkin cupcake with ganache and cream cheese frosting

What You Need To Make Small Batch Pumpkin Cupcakes


  • All-Purpose Flour
  • Baking Powder
  • Pumpkin Pie Spice
  • Salt
  • Granulated Sugar
  • Light Brown Sugar – I recommend light brown sugar because it does not have as much moisture content as dark brown sugar.  The cupcakes get enough moisture from the pumpkin.
  • Pumpkin – Pure canned pumpkin – and not pumpkin pie filling.  Pumpkin pie filling has added ingredients we don’t need for this cupcake recipe.
  • Egg
  • Unsalted Butter
  • Chocolate Chips – For the whipped ganache, and any chocolate intensity you prefer.
  • Heavy Cream – The heavy cream is for the whipped ganache and the whipped cream cheese.
  • Cream Cheese – For the whipped cream cheese frosting.  I do recommend full-fat cream cheese because of the solid texture and flavor.
  • Maple Syrup – The maple syrup is the sweetener I used in the cream cheese frosting.  However, use any sweetener you prefer.

Baking Equipment

  • Muffin/Cupcake Pan
  • Cupcake Liners – You could omit the cupcake liners and lightly grease and flour the cupcake wells.  I often use Pam Baking Spray with Flour for an easy option to grease and flour.
  • Mixing Bowls
Single pumpkin cupcake close up with cream cheese frosting

Whipped Dark Chocolate Ganache Frosting

If you have never had whipped ganache, it is a definite must-try.  It is easy to make and a great alternative to traditional buttercream frosting.  It is a light and airy topping that is easy to pipe and you can use any chocolate intensity you prefer to make it.

I chose dark chocolate morsels from Nestle for this recipe because the dark chocolate is a delicious pairing with the pumpkin cupcake.  Making the whipped ganache is easy, and there are two ways to make it:

  1. Warm the chocolate + cream – The chocolate and cream are heated together in the microwave until the chocolate starts to melt.  
  2. Warm just the cream – The heavy cream is warmed and poured over the chocolate chips. 

With either option, the steps after heating are the same:

  • Stir the ganache until it is smooth. 
  • Cool in the refrigerator until the ganache is nearly set. 
  • Whip until light and fluffy.
  • Make ahead to save some time!

Whipped Cream Cheese Frosting

Frosting number 2 is a frosting you would probably expect with a pumpkin cupcake – cream cheese.  Doubling up the frosting on this Small Batch of Pumpkin Cupcakes doubles up the flavor.  Chocolate and pumpkin go together, almost as good as pumpkin and cream cheese.  And when you combine all three, you are left with an extremely decadent cupcake.

I have combined chocolate and cream cheese before in the No-Bake Neapolitan Cheesecake.  There is a richness you get when combining the two flavors, along with a sweet tang.  And because chocolate and cream cheese go with Fall desserts like peanut butter and jelly, it only seemed fitting we add both frostings to the pumpkin cupcakes!

Tips For Making Small Batch Pumpkin Cupcakes

  • Make the frostings first – Both the Whipped Chocolate Ganache and Whipped Cream Cheese will set up even more if they have time to cool.  Make the frostings first then refrigerate until ready to  frost the cupcakes.
  • Bring the cream cheese to room temperature – I will go as far to say this is a must.  Trying to whip cold cream cheese until it is smooth is extremely frustrating.  There is nothing worse than tiny little lumps of cream cheese in your frosting!
  • Allow the chocolate ganache to cool and set – The ganache does need time to cool and set before it will whip up light and fluffy.
  • Use pure pumpkin – Pure pumpkin in a can is what we use for this recipe, not pumpkin pie filling.
  • Light brown sugar is best – Light brown sugar still imparts flavor, but not as much moisture as dark brown sugar.  We don’t need the extra moisture in these cupcakes.
  • Pumpkin pie spice is your friend – You can certainly whip up your own pumpkin spice blend.  But, it is the holidays, so make your life easier and use the premade store bought spice!
  • Cool the cupcakes completely before frosting – Seems obvious, but is also a test of willpower to let the cupcakes cool before devouring them!  
Double frosted pumpkin cupcake on a table

Common Questions For Making Small Batch Pumpkin Cupcakes

Can the recipe be doubled?

I have not tested a larger batch, but you can try it and let me know how the cupcakes turn out!

Why can’t I use pumpkin pie filling instead of pure canned pumpkin?

Pumpkin pie filling already has sugar and spices added to it. We want to use pure canned pumpkin so we can control the sweetness and spice.

I only have dark brown sugar. Will the recipe still work?

You can certainly try dark brown sugar. The bake time may take a minute or two more, and the cupcakes could potentially turn out a little more dense.

What is the best kind of chocolate to use for whipped chocolate ganache?

You can use any kind of chocolate baking bar or chip you prefer. I do recommend a good quality chocolate chip – like Nestle or Ghirardelli – if that is what you are using.

Can I substitute a different sweetener besides maple syrup in the cream cheese frosting?

Absolutely. I like using maple syrup because of its buttery sweet flavor. But feel free to swap in any sweetener you prefer.

What is the best way to store leftovers?

If you have any, frosted cupcakes are best stored covered in the refrigerator because of the cream cheese frosting. Unfrosted cupcakes will store fine covered at room temperature.

Four frosted pumpkin cupcakes on a platter

More Small Batch Desserts For Fall

Row of frosted small batch pumpkin cupcakes
Single pumpkin cupcake close up with cream cheese frosting
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5 from 2 reviews

Small Batch Pumpkin Cupcakes

Yield: 4 Cupcakes
Perfectly pumpkin-spiced and moist Pumpkin Cupcakes with Whipped Ganache Frosting are an easy small batch cupcake recipe.  The cupcakes are infused with plenty of pumpkin and cozy spices and topped with a whipped ganache and whipped cream cheese frosting.  A must-have dessert for your holiday menu!
Prep10 minutes
Cook20 minutes
Total30 minutes


  • 1 – Muffin/Cupcake Pan



  • 1/2 cup all-purpose flour
  • 1/2 teaspoon baking powder
  • 1/8 teaspoon salt
  • 3/4 teaspoon pumpkin pie spice
  • 3 tablespoons granulated sugar
  • 4 tablespoons light brown sugar
  • 1/4 cup pure canned pumpkin
  • 1 large egg
  • 2 tablespoons unsalted butter, melted

Whipped Ganache Frosting

Whipped Cream Cheese Frosting

  • 2 and 1/2 ounces cream cheese, room temperature
  • 2 tablespoons pure maple syrup
  • 1/4 cup heavy cream


Whipped Cream Cheese Frosting

  • In a small bowl, use a handheld mixer to whip the heavy cream into stiff peaks.
  • In another small bowl, use the handheld mixer to beat the cream cheese and maple syrup until smooth and creamy. Use a spatula to fold the whipped cream into the cream cheese. Refrigerate until ready to frost the cupcakes. The frosting will set up more as it refrigerates.

Whipped Ganache Frosting

  • In a small microwave-safe bowl add the chocolate chips and heavy whipping cream. Heat until the cream is warm, but not boiling over.
  • Remove the bowl from the microwave and let the mixture sit for 3-5 minutes to allow the chips to melt. Then stir the ganache until fully incorporated and smooth. Transfer to the refrigerator to allow the ganache to cool and set up. Keep in the refrigerator while your cupcakes are baking and cooling.
  • When ready to frost the cupcakes, use a handheld mixer and beat the ganache until light and fluffy – about 3-5 minutes.


  • Preheat oven to 350F degrees and adjust the oven rack to the middle position. Line a muffin pan with 4 cupcake liners.
  • In a small mixing bowl whisk together the flour, baking powder, baking soda, salt, cinnamon, ginger, and nutmeg.
  • In a medium mixing bowl, add both sugars and the pumpkin puree. Whisk together until well combined. Whisk in the egg, then the melted butter.
  • Sprinkle the dry ingredients over the wet ingredients and mix just until no dry streaks remain. Using a small spoon or cookie scoop, pour the batter in equal amounts into each of the cupcake liners.
  • Bake for 18 to 20 minutes or until the top of the cupcakes are spongy and a toothpick inserted in the middle comes out mostly clean. Cool the cupcakes in the pan set on a wire cooling rack for 5 minutes before transferring to the wire rack to cool completely.
  • To frost the cupcakes, you can use a knife to spread on layers of the Whipped Chocolate Ganache Frosting and Whipped Cream Cheese Frosting. Or, you can transfer each frosting to a piping bag and pipe on alternating layers of each frosting. The cupcakes are best enjoyed the day they are baked!
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  • Pumpkin – Depending on the brand, canned pumpkin can have different names, but is the same thing:  Pumpkin Puree, Pure Pumpkin, 100% Pumpkin, Organic Pure Pumpkin.  Just be sure it is not Pumpkin Pie Filling
Course: Dessert
Cuisine: American
Author: Erin Cernich

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