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.
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!
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).
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.
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.
Honey cinnamon frosting
This is such an easy and delicious substitute for a traditional cream cheese frosting!
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.
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!
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.
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
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.
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.
More pumpkin recipes you'll love!
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NOTE: If following the SCD diet, I suggest contacting the company to verify ingredients before using any prepackaged products.
Gluten Free 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
- 15 ounces farmer cheese room temperature
- ¼ cup honey
- ½ teaspoon ground cinnamon
- 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.
- 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.