Gluten-Free Pumpkin Cupcakes with Cream Cheese Frosting

Cupcake on two stacked plates with frosting colored to look like candy corn.
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These soft and moist pumpkin cupcakes are cozied up with warm spices and topped with a tangy cream cheese frosting that can be colored to resemble candy corn. This easy recipe is gluten-free friendly and perfect for fall - especially Halloween and Thanksgiving!

  • Author: alexandra
  • Prep Time: 45 minutes
  • Cooling Time: 1 hour
  • Cook Time: 20 minutes
  • Total Time: 2 hours 5 minutes
  • Yield: 12 cupcakes 1x
  • Category: cupcakes
  • Method: baking
  • Cuisine: American
  • Diet: Gluten Free



Pumpkin Spice Cupcakes

  • 2 cups, spoon and level (8 1/2 ounces) gluten-free all-purpose flour with xanthan gum
  • 1/4 cup, packed (1 7/8 ounces) brown sugar
  • 1/4 cup (1 3/4 ounces) granulated sugar
  • 2 teaspoons baking powder
  • 1/2 teaspoon baking soda
  • 1/4 teaspoon salt
  • 1 teaspoon ground cinnamon
  • 1/4 teaspoon ground all spice
  • 1/4 teaspoon ground ginger
  • 1/8 teaspoon ground nutmeg
  • 1/8 teaspoon ground cloves
  • 1 cup (8 ounces) pumpkin purée, room temperature
  • 1/2 cup (4 1/8 ounces) cream, room temperature
  • 1/4 cup (2 ounces or 1/2 stick) unsalted butter, melted
  • 3 large eggs, room temperature
  • 1 1/2 teaspoons vanilla extract

Cream Cheese Frosting

  • 8 ounces full-fat, block-style cream cheese, cold
  • 1 cup (8 ounces or 2 sticks) unsalted butter, softened
  • 4 cups (16 ounces) confectioner’s sugar
  • 1/2 teaspoon vanilla extract
  • heavy pinch of salt
  • yellow and orange gel food coloring (optional)
  • sprinkles or candy corn, for garnish (optional)


Pumpkin Spice Cupcakes

  1. Oven and pan prep: Preheat oven to 350ºF and line a standard-size 12-cup muffin pan with paper liners.
  2. Mix the dry ingredients: In a large mixing bowl, combine the gluten-free flour, brown sugar, granulated sugar, baking powder, baking soda, salt, cinnamon, all spice, ginger, nutmeg, and cloves. Whisk together thoroughly.
  3. Mix the wet ingredients: In a second, medium mixing bowl, whisk together the pumpkin puree and heavy cream until smooth. Keep whisking while slowly pouring in the melted butter. Finally, add the eggs and vanilla extract, continuing to whisk until everything is smoothly and evenly combined.
  4. Combine: Add the wet ingredient mixture to the dry and fold in with a spatula just until fully incorporated, avoiding overmixing. The batter will be fairly thick.
  5. Bake: Divide the cupcake batter evenly between the 12 lined muffin cups, smoothing the tops out lightly as you go. The muffin cups will be nearly full. Bake for 18-22 minutes, until a toothpick inserted into the center of one comes out clean or with just a few moist crumbs.
  6. Cool: Cool cupcakes in pan for about 10-15 minutes before moving to a wire rack to finish cooling. Cool completely before frosting.

Cream Cheese Frosting

  1. Beat butter and cream cheese: Using the bowl of a stand mixer fitted with the paddle attachment, beat the softened butter and cold cream cheese on low speed until well-combined, smooth, and creamy. Scrape down your bowl and beater as needed with a spatula.
  2. Add remaining ingredients. Switch mixer to the wire whip attachment and add the confectioner's sugar, vanilla extract, and salt. Continue to beat on low speed until everything is evenly incorporated into a smooth, thick frosting, again scraping down the bowl and beater as needed.
  3. Color (optional): If coloring frosting, divide into three bowls, with each portion being slightly smaller than the last. Using a spatula, mix yellow food color into the largest portion, and orange food color into the second largest portion, until both are as vibrant as you'd like them to be. Leave the smallest portion of frosting uncolored; this will be the white of your candy corn.
  4. Pipe: Using a piping bag and your tip of choice (I used a large round piping tip), pipe a single layer of yellow frosting onto each cupcake, followed by a layer of orange frosting, and finally a layer of white frosting. Garnish with sprinkles or candy corn as desired.


Ingredient Notes and Substitutions:

  • Regular all-purpose flour would likely work fine in this recipe if you don't need the cupcakes to be gluten-free.
  • The individual spices in this recipe (cinnamon, all spice, ginger, nutmeg, and cloves) can be substituted for a total of 1 3/4 teaspoons of pumpkin pie spice.
  • Light, regular, or heavy cream can be used for the cupcakes.
  • If using salted butter instead of unsalted, I'd suggest cutting back on the salt in the cupcake recipe to just 1/8 teaspoon, and skipping the added salt in the frosting entirely.
  • To quickly bring eggs to room temperature, put them in a cup and fill it with warm water. Let sit for about 5-10 minutes before using.

Storage and Shelf Life:

  • Cupcakes can sit at cool room temperature for about an hour or two, but for longer-term storage (and in warmer weather), they can be kept refrigerated in an airtight container for up to a few days.

Make ahead:

  • Cupcakes can be made in advance and stored in an airtight-container or zip-top bag. Cream cheese frosting is best if used fresh.

Extra Tips:

  • When coloring the frosting for this recipe, it's best to leave more frosting uncolored than you think you might need. You can always use some of it to make more yellow or orange frosting if you run out of those layers sooner than expected.
  • Piping the individual colors for this recipe is easiest if you have multiple piping bags, so you can simply move your piping tip between bags rather than cleaning and drying the same piping bag for each layer.
  •  To prevent runny frosting, always refrigerate any portions of frosting you're not actively working with. A brief 5-10 minutes of refrigeration can also help stiffen up a frosting that's a little too soft to pipe.