If you love fall-inspired desserts like apple pie crisps, pecan pie tarts, and anything pumpkin-flavored, you'll love these pumpkin spiced cupcakes with vegan cream cheese frosting. Spend the perfect Saturday afternoon baking these delicious cupcakes, celebrating the autumn season, and creating new memories in the kitchen with loved ones.

First, this recipe is completely vegan and can be made gluten-free if you swap the flour with almond flour or any gluten-free alternatives. These cupcakes are naturally sweetened with maple syrup and spiced with an aromatic blend of ground cloves, ground ginger, nutmeg, allspice, and cinnamon--the sweetest taste of fall.

Secondly, these pumpkin cupcakes are simple to make and only require ten minutes of prep, the perfect recipe to make with children. The frosting, in my opinion, is the best part. It's made with vegan cream cheese and powdered sugar-- it's a lot thicker and smoother than regular frosting. If you're like me, I make an extra bowl and keep it in the refrigerator to dip all sorts of foods into it like strawberries, pretzels, and spread the frosting on vegan muffins. Without further ado, put on your apron and bake these delicious and healthy vegan pumpkin cupcakes with cream cheese frosting.

Recipe Developer: Brittney, @thebananadiaries

Message from the recipe developer: "These incredibly moist vegan pumpkin cupcakes taste and look like fall. Packed with pumpkin spice and topped with vegan cream cheese frosting, they make the perfect fall treat."

Why we love it: When you take a bite into these cupcakes, you'll taste everything you love about fall. These treats are made with the perfect zesty pumpkin blend of ground cloves, ground ginger, nutmeg, allspice, and cinnamon. The best part is that these cupcakes are a lot healthier than traditional recipes and can be made gluten-free with the swap of flour.

Make it for: A special fall-inspired treat, or pack them in your children's school lunches to surprise them with a healthy pumpkin cupcake. Enjoy!
Prep Time: 10
Cook Time: 30
Total Time: 40 minutes

Healthy Pumpkin Cupcakes with Cream Cheese Frosting Recipe

Yields 12 cupcakes


Pumpkin Cupcakes:

  • 1 3/4 cup all-purpose flour or gluten-free 1:1 flour
  • 2/3 cup coconut sugar
  • 1/2 tsp baking soda
  • 1 tsp baking powder
  • 3 tsp cinnamon
  • 1 tbsp pumpkin spice (or blend of ground cloves, ground ginger, nutmeg, allspice, and cinnamon)
  • 1/4 tsp sea salt
  • 1 tbsp maple syrup
  • 1 cup pumpkin puree
  • 2 tablespoons ground flaxseed with 1/2 cup water
  • 1/2 cup coconut or almond milk mixed with 1 tsp apple cider vinegar
  • 1 tsp vanilla extract
  • 1/4 cup olive oil (or avocado oil or coconut oil)

Vegan Cream Cheese Frosting:

  • 3/4 cup vegan butter, softened (I use Miyoko’s, which is Paleo) or coconut oil
  • 1 8-oz. container vegan cream cheese (I use Miyoko’s, which is Paleo) or chilled coconut cream + 1 tbsp lemon juice
  • 3 cups powdered sugar *see not for Paleo/low sugar options
  • 1 tsp vanilla extract


  1. Preheat the oven to 350F and line a 12-tin muffin pan with cupcake liners.
  2. In a medium bowl, combine the flaxseed eggs with the pumpkin, coconut sugar, vanilla, maple syrup, coconut milk with apple cider vinegar, and olive oil using a spoon or hand mixer. Mix until well combined, then set aside.
  3. In a large bowl, whisk together the flour, spices, baking soda, baking powder, and sea salt. Fold in the wet ingredients to the mixed flour and mix with a spoon until well combined, being careful not to over mix and to make sure all clumps have been removed.
  4. Distribute pumpkin cupcake batter evenly among 12 cupcake liners, filling to about 3/4 of the way full.
  5. Bake the pumpkin cupcakes for 27-33 minutes, or until the toothpick comes out clean.
    Let cool completely before frosting.
  6. When you’re ready to frost, combine the vegan butter and vegan cream cheese in a large bowl with a hand mixer on high speed. Beat the two until light and fluffy.
  7. Add in about 1 cup of powdered sugar and continue beating, adding in additional sugar until it’s a thick frosting. Add in the vanilla extract and beat until well combined.
  8. Spoon frosting into piping bags and frost each individual cupcake.
  9. Keep cool to prevent the frosting from melting (I recommend storing in the fridge and when ready to serve, let the cupcakes come to room temperature for about 12-15 minutes).

*Eggs: To make a ground flaxseed egg, combine 2 tbsp of ground flaxseed with about 1/3 cup filtered water. Let the combination sit for 5-7 minutes.

*Sugar: To make this Paleo, use 3 cups powdered coconut sugar, which you can make by processing the coconut sugar in a food processor or 1/3 cup maple syrup. To make this lower in sugar, swap in 2 cup coconut flour for 2 cups powdered sugar, and keep 1 cup powdered sugar or 1 cup coconut sugar.

To make the pumpkin toppers: reserve about 1/2 cup of cream cheese frosting before you pipe the frosting onto the cupcakes. Mix in beet powder and turmeric powder together until you get a vibrant orange. Freeze the frosting for 10 minutes. Then remove from the freezer and roll into 12 small balls. Place the balls onto a piece of parchment paper and freeze again for 5 minutes. Use cinnamon sticks or twigs for the stems and top your cupcakes!


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