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    Home » Dessert Recipes

    Gluten Free Pumpkin Cupcakes

    Published: Oct 7, 2023 by Jennifer Brown · This post may contain affiliate links · Leave a Comment

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    These gluten free pumpkin cupcakes are soft, moist, perfectly spiced, and are topped with a luscious honey cinnamon frosting made with farmer cheese! The recipe is SCD, gluten free, grain free, refined sugar free, and low lactose.

    A cupcake on a table with other cupcakes and a pumpkin in the background.

    Fluffy, moist, and full of pumpkin flavors, this gluten free pumpkin cupcakes recipe with honey cinnamon frosting comes together quickly using pantry staples.

    Made with a perfect combination of spices, almond flour, pumpkin puree, and honey means a delicious and healthy pumpkin cupcakes recipe!

    These cupcakes are a fall baking must!

    Cupcake ingredients

    Ingredients for the gluten free pumpkin cupcakes on a light pink table.

    Almond Flour - As always, I recommend using blanched finely ground almond flour as it yields the best results.

    Pumpkin Puree - Make sure to use pumpkin puree and not pumpkin pie filling!! the only ingredient listed on the label should be pumpkin.

    Coconut Oil - If you prefer, olive oil can be used instead.

    How to make the pumpkin cupcakes

    Whisk together the almond flour, salt, baking soda, cinnamon, nutmeg, cloves, and ginger in a large bowl (photos 1 and 2).

    Mix the honey, pumpkin puree, lemon juice, coconut oil, and vanilla extract on low speed in the bowl of a stand mixer fitted with the paddle attachment (photo 3).

    A six photo collage showing how to mix the pumpkin cupcake batter and fill the muffin tin.

    With the mixer still on, add the eggs one at a time until fully incorporated (photo 4).

    Slowly add the almond flour mixture to the wet ingredients, stopping to scrape down the sides of the bowl as needed (photo 5). Don't overmix.

    The batter will be very thick.

    Evenly distribute the batter between 12 lined cupcake cups (photo 6) and bake until the tops are a light golden color and a toothpick inserted into the center of the cupcakes comes out clean.

    Perfectly baked cupcakes in a muffin tin.

    Allow to cool for 10 minutes before gently transferring the cupcakes to a wire rack to cool completely.

    To speed up the cooling process, feel free to place the cupcakes in the refrigerator.

    Make sure you let the pumpkin cupcakes cool completely before frosting or the frosting will just melt.

    A just frosted pumpkin cupcake.

    Honey cinnamon frosting

    This is such an easy and delicious substitute for a traditional cream cheese frosting!

    Frosting ingredients in a blender jar.

    Simply place the farmer cheese, honey, and ground cinnamon in a high speed blender and blend on high, stopping to scrape down the sides of the jar as needed, until smooth and creamy!

    You might be tempted to skip blending the frosting, but don't!

    Farmer cheese is very gritty, so it needs to be blended in order to achieve that smoothness.

    Tip: Making sure the farmer cheese is at room temperature will help it blend easier.

    What is farmer cheese and what if I can't find it?

    Farmer cheese, also known as dry curd cottage cheese, is made by pressing the curd until almost all of the liquid is gone.

    The end result is a gritty, soft cheese that's firmer than cottage cheese.

    I'm able to find it in my local Publix grocery store, typically next to the cream cheese, but it can be difficult to source depending on your area.

    If you are following the specific carbohydrate diet (SCD), then you can strain SCD yogurt for 24 hours until it's the consistency of cream cheese and use it instead.

    A ground cinnamon dusted cupcake on a pink table with other cupcakes around it.

    For those of you not following the SCD diet, feel free to use traditional cream cheese in place of the farmer cheese.

    Another option is to use a different frosting altogether!

    My Vanilla Italian Meringue Buttercream is a perfect option.

    If you want to really pump up that pumpkin flavor, then feel free to use my Pumpkin Buttercream Frosting!

    Assembly

    Once the cupcakes have cooled, use a knife or piping bag to frost each one.

    I garnished each with a light dusting of ground cinnamon and a cinnamon stick.

    A half eaten cupcake on a table surrounded by other cupcakes.

    If making these for kids or Halloween, try topping them with plastic spiders, skulls, or pumpkins. Walmart or Dollar Tree normally have a lot!

    Frequently asked questions

    How should I store the cupcakes?

    Frosted cupcakes will need to be covered and stored in the refrigerator for up to 3 days. When cold, the frosting firms up quite a bit. I suggest allowing the cupcakes to come up to room temperature before serving.

    Can I freeze the cupcakes?

    Unfrosted pumpkin cupcakes can be frozen for up to 3 months. I suggest freezing on a baking sheet first, then transferring to a freezer safe bag. Thaw in the refrigerator overnight, bring to room temperature, and frost before serving.

    A close up of a pumpkin cupcake with other cupcakes in the background.

    More pumpkin recipes you'll love!

    • Pumpkin Spice Cake Bites
    • Mini Pumpkin Cheesecakes
    • Almond Flour Pumpkin Bread
    • Pumpkin Blondies

    If you made this recipe, be sure to leave a comment and star rating below! This is the best way you can help support me and my blog!

    Follow me on facebook and instagram . Tag @thehealthierbite and #thehealthierbite so I can see your yummy creations!

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    NOTE: If following the SCD diet, I suggest contacting the company to verify ingredients before using any prepackaged products.

    Recipe

    A cupcake sprinkled with ground cinnamon on a table.

    Gluten Free Pumpkin Cupcakes

    by: Jennifer Brown
    These gluten free pumpkin cupcakes are soft, moist, perfectly spiced, and are topped with a luscious honey cinnamon frosting made with farmer cheese! The recipe is SCD, gluten free, grain free, refined sugar free, and low lactose.
    Print Recipe Pin Recipe Save Recipe Saved!
    Prep Time 10 minutes mins
    Cook Time 25 minutes mins
    Frosting 5 minutes mins
    Course Dessert
    Cuisine American
    Servings 12
    Calories 305 kcal

    Ingredients
      

    Pumpkin Cupcakes

    • 3 cups blanched finely ground almond flour
    • 1 teaspoon baking soda
    • 1 teaspoon fine sea salt
    • 2 teaspoons ground cinnamon
    • ½ teaspoon ground ginger
    • ½ teaspoon ground nutmeg
    • ¼ teaspoon ground cloves
    • 3 large eggs room temperature
    • 1 cup pumpkin puree
    • ⅓ cup honey
    • 2 Tablespoon melted coconut oil not hot
    • 1 Tablespoon vanilla extract
    • ½ teaspoon lemon juice

    Frosting

    • 15 ounces farmer cheese room temperature
    • ¼ cup honey
    • ½ teaspoon ground cinnamon

    Instructions
     

    Pumpkin Cupcakes

    • Preheat the oven to 325F. Line 12 cups of a standard muffin tin with liners and set aside.
    • Whisk together the almond flour, baking soda, salt, cinnamon, ginger, nutmeg, and cloves in a large bowl. Set Aside.
    • On low speed, mix the pumpkin puree, honey, coconut oil, vanilla, and lemon juice in the bowl of a stand mixer fitted with the paddle attachment.
    • With the mixer still running on low, add the eggs one at a time until fully incorporated.
    • Slowly add the almond flour mixture and continue running on low speed just until combined. Don't over mix. the batter will be very thick.
    • Evenly distribute the batter among the lined muffin cups, filling until almost the very top.
    • Place the muffin pan on the middle rack of the oven and bake for 25 to 35 minutes or until the cupcakes have puffed up, are golden in color, and a toothpick inserted into the center comes out clean.
    • Allow to cool for 10 minutes in the pan before turning out onto a wire rack to cool completely. For a faster cool time, feel free to place in the fridge. Do not frost the cupcakes until they've cooled completely.

    Frosting

    • Place the room temperature farmer cheese, honey, and cinnamon in the jar of a high speed blender and blend on high until smooth and creamy. You may need to use a taper to facilitate blending or stop to scrape down the sides of the jar a few times.
    • Use a knife or piping bag to frost the cupcakes. If you'd like, garnish with a light dusting of ground cinnamon.

    Notes

    Store frosted cupcakes covered in the refrigerator for up to 3 days. Once cold, the frosting firms up quite a bit, I suggest allowing the cupcakes to come up to room temperature before serving. 
     
    The nutritional information calculated in this recipe are just an estimate. The photos and content above are copyright protected. Please do not use my photos. Please do not copy this recipe and share it on your own website or social media channels. If you wish to tell people about this recipe, you can provide a link back to my blog rather than copying the recipe. Thank you! XO, Jen

    Nutrition

    Calories: 305kcal | Carbohydrates: 22g | Protein: 13g | Fat: 20g | Saturated Fat: 5g | Polyunsaturated Fat: 0.3g | Monounsaturated Fat: 1g | Cholesterol: 58mg | Sodium: 446mg | Potassium: 73mg | Fiber: 4g | Sugar: 15g | Vitamin A: 3246IU | Vitamin C: 1mg | Calcium: 77mg | Iron: 2mg
    Keyword almond flour cupcakes, cinnamon frosting, gluten free spice cupcakes
    Did you make this recipe?Let me know how it was by leaving a comment and star rating below!

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