Pumpkin Chocolate Chip Cookies are melt-in-your mouth soft, easy to make, and secretly healthy.  This treat is full of pumpkin flavor and is gluten-free, vegan, and Paleo. This recipe will become a new favorite for the Fall and Thanksgiving season!

Want a few other healthy pumpkin recipes?  You might also enjoy these Healthy Pumpkin Muffins, these Paleo Pumpkin Pancakes, and this Coconut Flour Pumpkin Bread.

Gluten-free pumpkin cookies in a stack with a bite taken out.

Testing The Recipe

There are a few friends in my life who are rather honest with me when it comes to critiquing recipes.

Because of this, I decided to bring over the few test batches of these pumpkin chocolate chip cookies.

I can handle an obscene amount of fall spice flavor – well beyond the average Jane.

And on the flip side, Cohl cannot STAND anything with too much cinnamon and spice.  (WHAT?!?)

Also, I had already burnt out my taste buds distinguishing between recipes.  I needed some fresh taste buds to tell me their opinion.

So I loaded up the two test batches of these light and fluffy cookies:

Test Batch #1: Some made with coconut flour and almond flour.

Test Batch #2: Some made with cassava flour.

It was time to do a little taste testing!!

Pumpkin chocolate chip cookie recipe with pumpkin puree and dark chocolate chips.

Healthy Pumpkin Cookies Recipe Results

While I will admit, the first round of cassava flour cookies were definitely not the best.  Although, I did make another batch later that turned out fabulous.

It was unanimously decided that the coconut and almond flour pumpkin cookies recipe was the winner.

The cassava flour ones rose beautifully and looked gorgeous.  However, they lacked a bit of flavor.

Whereas the almond and coconut flour pumpkin puree cookies were perfectly chewy AND tasted incredible.

Vegan pumpkin cookies with pumpkin puree, pumpkin spice, and coconut sugar.

How to Make

Now that we have a clear winner, how exactly do you make a healthy pumpkin chocolate chip cookie recipe?

If you do a bit of Paleo and gluten-free baking you probably have all of these ingredients.

However, if you can still easily find the ingredients if you are a newbie to this Paleo and vegan world.  Almost all of the ingredients needed in this recipe can be found on Amazon or at your local specialty grocery store.

 Steps: (See recipe card for more in-depth information and ingredient amounts.)

  1. Preheat your oven to 350 degrees.
  2. Whisk together the wet ingredients.
    • Pumpkin puree, coconut oil (or vegetable oil), maple syrup, a flax egg, and vanilla extract.
  3. Toss together your dry ingredients.
    • Tapioca starch, almond and coconut flour, baking soda, coconut sugar, and salt.
  4. Combine the wet and dry ingredients together with the semi sweet chocolate chips.
  5. Place the cookies on a baking sheet with parchment paper or a baking mat.
  6. Bake in preheated oven for about 12 minutes.
  7. Place on wire racks to cool before serving.

You might also enjoy these Paleo pumpkin recipes:  Paleo Pumpkin Pancakes, Coconut Flour Pumpkin Bread, and these Paleo Pumpkin Muffins.

Healthy pumpkin cookies in a stack with a bite taken out.Ingredients

What ingredients will you need for this delicious Fall dessert?

  • Pumpkin Puree – You can either choose to make your own homemade pumpkin puree or use a canned kind instead!
  • Almond flour – Please, please be sure to get Bob’s Red Mill blanched and super fine almond flour.  Other almond flour brands may have a texture that is too gritty.
  • Coconut flour – Most coconut flours are pretty similar so you can pick up whatever you happen to find in your store.
  • Arrowroot starch – Tapioca flour will work as a good substitute here, too.  I would not recommend using corn starch, though!
  • Flax egg – This is necessary if you want to make these vegan.  However, you can always use a regular egg in this recipe instead.
  • Coconut oil – Vegetable oil will also work if you’re dairy-free.  Or, you can also use butter if you are not vegan.
  • Pumpkin Pie Spice – I found this blend tasted WAY better than the normal spices.  However, feel free to substitute cinnamon, nutmeg, and a pinch of cloves instead.
  • Paleo Chocolate Chips – If you are not dairy, grain, gluten, or soy-free you can use regular semi sweet chocolate chips.

Kitchen Tools and Utensils Needed

There are not too many unique kitchen gadgets needed to make this recipe.

A few items you probably already have, but may want to double check, include:

Pumpkin Chocolate Chip Cookies Recipe on a grey backdrop with chocolate chips and pumpkin puree.

How Can You Evolve This Recipe

These are already free of glutens, grains, dairy, soy, and refined sugar.  There are a few tweaks and changes you can make:

  • If you do not have coconut oil or are not dairy-free, feel free to use butter.
  • Add in some nuts such as pecans or walnuts to give them a bit of a crunch.
  • Swap out the Paleo chocolate chips for milk or white chocolate chips.
  • Feel free to use honey or agave nectar in place of the maple syrup.  (The cookies will taste a bit different!)
  • Make a Pumpkin Chocolate Chip Cookie Bread or Oatmeal Chocolate Chip Cookies instead!

Want More Gluten-Free Dessert Recipes?

Paleo Chocolate Chip Cookies with Pecans

No Bake Pumpkin Pie Balls | Gluten Free, Vegan

Almond Flour Chocolate Chip Cookies

The Best Grain-Free Vegan Pumpkin Pie

Gluten-Free Chocolate Chip Cookies

Pumpkin Spice Cake Pops

Tap stars to rate!

4.39 from 21 votes

Pumpkin Chocolate Chip Cookies | Vegan, Paleo

Pumpkin Chocolate Chip Cookies are melt-in-your mouth soft, so easy to whip up, and made healthy by using gluten-free flours, dairy-free and vegan coconut oil, and Paleo chocolate chips!
Pumpkin chocolate chip cookie recipe with pumpkin puree and dark chocolate chips.
Yield 15 cookies
Prep 16 minutes
Cook 14 minutes
Total 30 minutes
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  • 1 cup almond flour blanched, super fine
  • ¼ cup coconut flour
  • ¼ cup arrowroot starch
  • ½ cup coconut sugar
  • ½ tsp. baking soda
  • ¼ tsp. salt
  • 1 ¼ tsp. pumpkin pie spice
  • ¼ cup coconut oil melted
  • ½ cup pumpkin puree homemade or canned
  • ¼ cup maple syrup pure
  • 1 flax egg*
  • 1 ½ t. vanilla extract
  • ¾ cup chocolate chips Paleo approved


  • Preheat oven to 350 degrees.
  • In a medium-large mixing bowl whisk together almond flour, coconut flour, arrowroot starch, coconut sugar, baking soda, salt, and pumpkin pie spice.
  • In a separate large mixing bowl combine melted coconut oil, pumpkin puree, maple syrup, flax egg, and vanilla extract. Mix with a handheld or stand mixer on medium speed for 1 minute or until well combined.
  • Add dry ingredients into wet ingredients and mix at medium speed for 1 minute.
  • Stir in chocolate chips by hand.
  • Line a baking sheet with parchment paper and place 1 ½ tablespoons-sized balls of cookie dough 2 inches apart. Press balls of dough down until the dough is about ¾ inch thick. (Cookies will not spread too much, so this step will help you make the shape of the finished cookies you want!)
  • Bake in preheated oven for 12-14 minutes or until cookies are done.
  • Let cookies sit at room temperature until completely cooled before serving. 
Last step! If you make this, please leave a review letting us know how it was!

Tap stars to rate!

4.39 from 21 votes


*1 Tbsp. ground flaxseed meal + 2 ½ Tbsp. warm water.  Whisk and let sit for at least 10 minutes before using.
Cookies keep well for 3-4 days at room temperature in an open container and up to 5 days in the refrigerator.


Calories: 174kcal, Carbohydrates: 20g, Protein: 2g, Fat: 10g, Saturated Fat: 5g, Cholesterol: 1mg, Sodium: 98mg, Potassium: 37mg, Fiber: 2g, Sugar: 13g, Vitamin A: 1290IU, Vitamin C: 0.4mg, Calcium: 39mg, Iron: 0.7mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Made this recipe?Leave a comment below!
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Recipe Rating


  1. Havenot made yet but definitely will and I will let you know, but they look delicious
    I was wondering if I wanted to use butter instead of coconut
    oil would the measurement of 1/4 cup be the same?

  2. These are insanely good!! Followed the recipe exactly and they turned out so good! Thank you so much for the recipe!!

    1. Yay! So happy you’re enjoying the recipe. It’s one of our faves, too! Thanks for taking the time to leave a comment, Julie 🙂

  3. These are delicious!! I am allergic to almonds so used 1/2 sunflower flour and 1/2 pumpkin flour!! Loved them. Thank you so much!

    1. That’s great to know that it worked, Laura! My husband recently discovered he has a mild almond sensitivity so I’ve been looking for good flour substitutes. Will have to try that out!

  4. 5 stars
    These came out Delicious! 😋 Moist… Aromatic … I halved the sugar amount and it didn’t affect the end result … I made half the batch with walnuts and the other half without …. Thanks for sharing! 🤩