Mimi's Organic Eats » Recipes » Fall » The Best Gluten Free Pumpkin Chocolate Chip Cookies
The Best Gluten Free Pumpkin Chocolate Chip Cookies
Cookies • Gluten Free • No Seed Oils • High Altitude • Fall • Thanksgiving | Published October 24, 2023 by Mimi Council
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These are absolutely the best Gluten Free Pumpkin Chocolate Chip Cookies! Soft, chewy, naturally eggless (bonus) with pumpkin spice, pumpkin seeds, semi sweet chocolate chip, and a sprinkle of flaky sea salt on top!
If you’re looking for more amazing gluten free desserts, try out some of my other favorites like my Eggless Chocolate Dipped Almond Cookies, Dark Chocolate Coconut Cups, or my Vegan Chocolate Peanut Butter Ice Cream Bars.

Table of Contents
These gluten free pumpkin cookies are one of my favorite cookies! I'm not even gluten free, so that's saying a lot! They are soft, chewy, and you don't need any gluten free flour blends as I just use a mix of organic almond flour and coconut flour! These cookies are filled with chocolate chips, pumpkin seeds, and topped with a flaky sea salt.
This recipe is so flexible, as these are naturally eggless pumpkin cookies, so if you're egg free, don't worry I got you! These can also be made vegan with just one simple adjustment (swap the butter for vegan butter or shortening). So, if you are gluten free or just limiting gluten and want to indulge in the flavor of the season, these are the best gluten free Pumpkin Chocolate Chip Cookies!

Why You'll Love This Recipe
No Gluten Needed: I’m usually not one to choose gluten free if there is a gluten filled option. But, I would choose these cookies over any pumpkin cookie any day! I feel incredibly confident calling these the best Gluten Free Pumpkin Chocolate Chip Cookies!
Soft & Chewy: These are classic soft and chewy cookies! The pumpkin makes these cookies soft and chewy, something that sometimes gluten free cookies can lack depending on the flour type used.
Perfectly Spiced: These are not overly pumpkin spiced, but just the right amount. I use a small amount of pumpkin spice, in addition to the pumpkin and pumpkin seeds. This trio makes these cookies incredibly flavorful and delicious without being too spicy.
Sweet & Salty: I love a sweet salty cookie! It’s my absolute favorite combo. I add a little sprinkle of flaky sea salt on top of these cookies for the perfect balance of sweet and salty.

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Ingredients
- Butter: I use Organic Valley Salted Butter. But, if you want to make these vegan you can use organic vegetable shortening or your favorite vegan butter. I've tested this both ways.
- Dark Brown Sugar: I use my homemade organic dark brown sugar, but store bought is also okay.
- Cane Sugar: I use organic cane sugar.
- Vanilla Extract: My favorite is Simply Organic.
- Pumpkin: I use organic pumpkin puree, this also makes these cookies naturally eggless as pumpkin is a great egg replacer.
- Almond Flour: I use organic almond flour, this gives these cookies great chewy texture combined with the pumpkin.
- Coconut Flour: I use organic coconut flour mixed with the almond flour, this is one of my favorite gluten free flour blends.
- Baking Soda: I use baking soda. Be sure to read my post the Difference Between Baking Soda and Baking Powder for more info on leavening agents.
- Salt: Make sure to use a fine sea salt.
- Pumpkin Spice: I use my homemade pumpkin spice mix, but you can also use store bought.
- Chocolate Chips: I use organic semi sweet chocolate chips, but you can also use dark chocolate if you prefer.
- Pumpkin Seeds: I add organic roasted and salted pumpkin seeds for some delicious crunch and added health benefits.
- Flaky Sea Salt: These cookies are topped with flaky sea salt for a sweet and salty cookie that I'm obsessed with. This part is optional, so feel free to leave it off if you want.

Tools Needed
- Scale: Always use a digital food scale for the best results.
- Stand Mixer: I use my stand mixer for ease, but you can also use a hand mixer if you prefer.
- Baking Sheets: You'll need two half sheet pans.
- Parchment Paper: I always use parchment paper for the best results, my favorite nontoxic parchment paper is Kana.

Step by Step Instructions
Step 1
Preheat the oven to 375°F. Line 2 baking sheets with parchment paper.
Step 2
In the bowl of a stand mixer fitted with the paddle attachment, add the butter, brown sugar, cane sugar, and vanilla extract. Mix on low until combined.
Add the pumpkin purée, almond flour, coconut flour, pumpkin spice, baking soda, and sea salt in that order. Mix on low until combined.
Add the chocolate chips and pumpkin seeds and mix to combine completely.






Step 3
Using your hands (or a cookie scoop) form cookie dough into 24 balls and place on the prepared baking sheets. Flatten them slightly so they are about 2 inches in diameter. The cookies will turn out to be the about the size you form them, there’s really no spread!
Step 4
Bake for 12 to 14 minutes or until the cookies are golden brown around the edges and bottom. Top with flaky sea salt immediately after coming out of the oven. Allow to cool completely on the baking sheets. (If you're baking at high altitude, be sure to check the Notes at the bottom of the recipe for high altitude baking instructions).

FAQ's
You can easily make this recipe vegan by swapping out the butter for vegan butter.
Yes, all my recipes can be made at high altitude with just one simple adjustment. If you are baking above 5,000 feet then be sure to check the Notes at the bottom of the recipe for the high altitude baking time.
When you open a can of pumpkin for this recipe, you'll have extra pumpkin. The pumpkin will stay good in the fridge for up to 5 days, so try out some of my other favorite pumpkin recipes like Vegan Pumpkin Spice Almond Butter Cookies, Buttermilk Pumpkin Waffles, or make your dog dinner with my Chicken and Pumpkin Dinner for Dogs!

Craving More?
- 10 Must Bake Pumpkin Spice Recipes
- Pumpkin Peanut Butter Dog Cookies
- Vegan Pumpkin Spice Banana Bread
- Homemade Pumpkin Pie Spice Mix
- Vegan Pumpkin Spice Almond Butter Cookies

The Best Gluten Free Pumpkin Chocolate Chip Cookies
Mimi CouncilIngredients
- 113 grams salted butter (softened)
- 113 grams dark brown sugar (packed)
- 57 grams cane sugar
- 1 teaspoon vanilla extract
- 113 grams pumpkin purée
- 198 grams almond flour
- 71 grams coconut flour
- 1 teaspoon pumpkin spice
- ½ teaspoon baking soda
- ½ teaspoon fine sea salt
- 198 grams semi sweet chocolate chip
- 57 grams roasted and salted pumpkin seeds
- Flaky sea salt (optional)
Instructions
- Preheat the oven to 375°F. Line 2 baking sheets with parchment paper.
- In the bowl of a stand mixer fitted with the paddle attachment, add the butter, brown sugar, cane sugar, and vanilla extract. Mix on low until combined.
- Add the pumpkin purée, almond flour, coconut flour, pumpkin spice, baking soda, and sea salt in that order. Mix on low until combined.
- Add the chocolate chips and pumpkin seeds and mix to combine completely.
- Using your hands (or a cookie scoop) form cookie dough into 24 balls and place on the prepared baking sheets. Flatten them slightly so they are about 2 inches in diameter. The cookies will turn out to be the about the size you form them, there’s really no spread!
- Bake for 12 to 14 minutes or until the cookies are golden brown around the edges and bottom. Top with flaky sea salt immediately after coming out of the oven. Allow to cool completely on the baking sheets.
- Store in an airtight container for up to 7 days.
Video

Notes
Nutrition
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I love how soft and chewy these are and could not tell they are gluten free. The hint of salt made them so fantastic!