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Gluten Free Pumpkin Cookies

This small batch recipe for gluten-free Pumpkin Cookies makes cookies that are soft, sweet, and full of warm spices. The coconut sugar perfectly complements the pumpkin, creating the ultimate fall treat and can be easily doubled.

On a white plate, on a white counter, 7 gluten free pumpkin cookies sitting on a white plate, spread out like a flower. In the background there are some leftover spices and cookie crumbs.

Why I Love These Gluten Free Fall Cookies

These healthy cookies are like little pieces of Fall in a heavenly bite. They are absolutely packed with warm Fall spices and the texture is so special. They are chewy and crisp on the outside, and soft and cake-like on the inside. The coconut sugar gives a subtle caramel taste that is unbeatable! These cookies are certainly a staple cookie for this Fall, perfect to enjoy alongside you late morning coffee.

A hand holds a chewy gluten free pumpkin cookie that has had a bite taken out of it. In the background, on the counter top, the cooling rack is sitting with extra cookies on top of it. Some spices are scattered on the counter too.

Ingredients and Substitutions

Ingredients required for gluten free pumpkin spice cookies on a white marble counter. There is a carton of eggs with 1 egg laying outside of the carton on the counter, a bowl of gluten-free flour, a plate with butter, a bowl with coconut sugar, a small bowl of pumpkin puree. 
There is also measuring spoons with vanilla extract, another spoon with baking powder, one with baking soda and another with pumpkin spice.

Can I use fresh pumpkin puree instead of canned?

Yes, fresh pumpkin puree should work in this recipe. Canned pumpkin is a fairly thick puree.

If using homemade fresh pumpkin puree, make sure the consistency is similar to that of canned pumpkin puree to avoid adding additional moisture to the recipe. I recommend baking the pumpkin in the oven at 370°F for about 30 to 45 minute, and then blend well in a blender or food processor.

Can I use regular flour in this recipe?

If you don’t need to follow a gluten-free diet, regular flour can be substituted in this recipe.

You should be able to substitute regular all-purpose baking flour at a 1:1 ratio replacing the gluten-free flour.

What can I use instead of coconut sugar?

Coconut sugar has an almost caramel-ly flavor which makes it perfect for pumpkin treats.

Dark brown sugar or maple sugar (granulated maple sugar not syrup) make the best substitutes for coconut sugar in this recipe.

If substituting, measure using volume measurements instead of weight-based measurements eg cups instead of grams.

On a white counter top there is a glass bowl filled with cookie dough, a baking tray is lined with baking paper. On top of the baking tray there are 4 balls of cookie dough and another balls is sitting in a bowl containing coconut sugar. There is an ice cream scoop with some more cookie dough in it, waiting to be rolled in sugar and placed on the tray. 
There are spices laying on to of the counter.

How to make these into Vegan Gluten Free Pumpkin Cookies

This recipe was tested using softened coconut oil (not melted) in place of butter and a flax egg in place of the egg yolk.

To make the flax egg, stir together 1 tbsp. ground flax seed with 2 tbsp. hot water and let it sit for about 5 minutes before mixing it into the dough.

The cookies will not flatten out as much using vegan substitutions, but they will still be delicious.

Some of the ingredients required to make these gluten free fall cookies. On a white counter top, there is a glass bowl filled with coconut sugar, a stick of soft, but not melted butter is sitting on top. There is a small white bowl filled with pumpkin puree and a carton of eggs can be seen in the corner, but you cannot see the full carton. 
Some wooden spoons are resting with some spice in them, like pumpkin spice and salt and more spices are scattered across the work space. In the bottom corner you can see the metal beaters for the electric whisk

How to Make Pumpkin Spice?

If you have ground cinnamon, nutmeg, ground cloves, and ground ginger on hand, you can make pumpkin pie spice at home.

Simply combine 1 tsp. of ground cinnamon, ¼ tsp. of ground nutmeg, 1/8 tsp. of ground cloves, and ¼ tsp. of ground ginger in a small bowl and stir together.

Measure out ½ tsp. of the spice mixture for this recipe and store leftovers in an airtight container.

A baking tray lined with greaseproof paper has 8 cooked pumpkin spice cookies on top. There are a few spices like cinnamon stick and star anise laying around the counter.

Gluten-Free Pumpkin Cookies: Pro Tips

  • Always use softened, not melted, butter. Melted butter would cause the cookies to spread too much. If substituting coconut oil or another vegan alternative to butter, it is also recommended to soften but not melt this ingredient.
  • A stand mixer can be used instead of a handheld electric mixer.
  • Check on the cookies after 11 minutes of baking. Fully baked cookies, should flatten out, have a crinkly top, and crispy-looking, well-formed edges.
A white plate sitting on a white marble counter has 7 pumpkin cookies on top, spread out like a flower. In the background there is a wire rack with the extra cookies cooling on top.
  • Allow the cookies to cool on the pan and then transfer using a spatula. The pumpkin in the cookies causes them to be fairly fragile before they have cooled.
  • When you finish mixing the dough, it is fairly soft. Chilling it for 10-15 minutes before rolling it will help it form into uniform balls.
  • Make sure you purchase canned pumpkin puree and NOT pumpkin pie filling. Even though we only use a small amount in this recipe, pumpkin pie filling tends to be waterier and will cause the cookies to be overly sweet.
  • Top with a cream cheese frosting or a drizzle of icing to make these cookies extra tasty!
6 fall cookies stacked on top of each other, on a white marble counter. Another cookie  with a bite out is sitting next to the stack and there is a wire rack in the background with more cookies cooling on top of it.

Frequently Asked Questions

What type of gluten-free flour should I use?

Using a gluten-free all-purpose baking flour that measures 1:1 with regular flour will yield the best results. I tested King Arthur Gluten-Free Measure-to-Measure Flour and Bob’s Red Mill Gluten-Free 1:1 All-Purpose Flour.
While weights varied slightly, results were similar with both flours when measuring with loose and level scoops.

What is the best way to store these gluten free Pumpkin cookies?

Once they have cooled, make sure they are in an air tight container and they can live in the refrigerator fro up to 5 days – I’ll be super impressed if you manage to keep them for that long though!

Can I use Pumpkin Pie Filling instead of Pumpkin Puree?

The short answer – no. I wouldn’t recommend it. Pumpkin pie filling is often much more watery than puree and a lot sweeter. It will change both the taste and texture of the cookie.

A white marble counter with a rectangle wire rack with lots of Fall pumpkin cookies on top. The spices used inside of the recipe like cinnamon and cloves are laying around the cookies on the counter.

Hungry for More Delicious Fall Cookies?

If you loved these gluten free Pumpkin Cookies as much as me and would like to try more of my Fall themed cookies, then try my delicious Pumpkin Molasses Cookies, or even my easy Pumpkin Oatmeal Cookies.

If you want to step away from the pumpkin (although I couldn’t at this time of year) check out my warm and spiced Carrot Cake Cookies. They are full of yummy textures and go so well with a hot cup of tea on a crisp Fall morning.

I hope you loved this recipe as much as me, leave a comment below if you made them! Don’t forget to follow me on Facebook and Instagram, I love seeing your recreations of my desserts! You can also follow me on Pinterest to keep up to date with all the latest JavaCupcake Blog news!

Gluten-Free Pumpkin Cookies

Gluten-Free Pumpkin Cookies

Yield: 16
Prep Time: 25 minutes
Cook Time: 15 minutes
Additional Time: 5 minutes
Total Time: 5 minutes

These gluten-free pumpkin cookies are soft, sweet, and full of warm spices. The coconut sugar perfectly complements the pumpkin, creating the ultimate fall treat. This recipe is a ‘small-batch’ making 16 cookies but can easily be doubled.


  • ½ cup salted butter, softened (4 ounces, 110 g)
  • ¾ cup coconut sugar (145 g)
  • 1 egg yolk, large
  • 2 tbsp pumpkin puree (30 g)
  • ½ tsp vanilla
  • 1 ¼ cups gluten-free all-purpose flour (155 g)
  • ½ tsp baking soda
  • ¼ tsp baking powder
  • ¼ tsp salt
  • 1 tsp pumpkin pie spice
  • 1 Tbsp coconut sugar
  • 1 Tbsp granulated sugar
  • ¼ tsp pumpkin pie spice


  1. Preheat the oven to 350 F and line a large baking sheet with
    parchment paper. Set aside.
  2. In a large mixing bowl, cream the softened butter and
    coconut sugar until smooth and fluffy using a handheld electric mixer.
  3. Add the egg yolk, vanilla, and pumpkin puree to the mixing
    bowl. Beat together until smooth.
  4. In a separate bowl, combine dry ingredients (flour, baking
    soda, baking powder, salt, and pumpkin pie spice). Stir together until all dry
    ingredients are well incorporated.
  5. Add the dry ingredients into the bowl with the wet
    ingredients and mix them together, using the handheld mixer, until there are no
    streaks or lumps. Avoid overmixing.
  6. Place the mixing bowl with the cookie dough in the fridge
    for about 10-15 minutes to chill.
  7. In a small bowl, combine 1 tbsp. coconut sugar, 1 tbsp. of
    granulated sugar and ¼ tsp of pumpkin pie spice. Mix together and set aside.
  8. Once the dough has chilled, scoop the dough using a 1-ounce
    cookie scoop and roll the dough between your hands.
  9. Roll each ball of dough in the sugar mixture and then roll
    between hands until it is an even shape. Place on the lined baking sheet.
  10. Leave about 3 inches between the cookies because the dough
    will spread while baking. You should be able to fit 8 cookies on a large baking
    sheet. You will need two baking sheets if you want to cook all the cookies at
    the same time, otherwise, you will need to cook them in batches.
  11. Place the baking sheet in the center rack of the oven and
    bake for 11-14 minutes or until the cookies flatten out, develop a crackly look
    on top, and the edges begin to become firm.
  12. Remove from the oven and allow to cool on the baking sheet
    for at least 5 minutes before transferring using a spatula to a wire cooling
  13. Store cookies in an airtight container in the fridge for
    about 5 days. Cookies can be stored on the countertop but will become soft
    after a day or two.


This recipe was developed at about 5000 ft elevation. In theory, this may affect bake time. For this recipe, moderate elevation change probably won’t make much of a difference, but for reference, these in the photos baked for exactly 13 minutes.

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