Paleo Pumpkin Chocolate Chip Cookies are a delicious gluten & dairy free fall dessert. Soft, chewy & packed with chocolate – everyone will love this recipe! These healthy cookies are great with a cup of coffee or served with some ice cream.

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These healthy pumpkin cookies are super soft and chewy. They pretty much melt in your mouth, and have the perfect amount of warm fall flavors and sweet dark chocolate chunks! (The best part about any cookie is obviously the chocolate!)
These pumpkin cookies are gluten, grain, and dairy free although you wouldn’t even notice! They’re perfect for enjoying as a simple fall dessert or with a Paleo Pumpkin Spice Latte as an afternoon pick me up.
We love all things pumpkin, and these pumpkin cookies might be one of our fav pumpkin recipes.. they’re right up there with these amazing Pumpkin Protein Pancakes or this Pumpkin Chicken Chili.

Let me tell you – these cookies were definitely a labor of love.
I’ve made regular (not so healthy) pumpkin chocolate chip cookies before and they were so delicious that it’s had me thinking about making a healthy version for years. Turns out this is much easier said than done.
Ingredients for Paleo Pumpkin Cookies
To make these paleo pumpkin cookies you’ll need:
- coconut oil
- pumpkin puree
- maple syrup
- almond flour, coconut flour
- cinnamon, ground ginger, nutmeg, cloves
- baking soda
- sea salt
- dark chocolate
You can find substitutions for all of these ingredients below in the green shaded substitutions box.

Because these cookies are gluten/grain free, you need to press them down (gently!) before baking them into small circles. They won’t flatten on their own.

After the cookies are properly flattened on the baking sheet and you have to wait what seems like forever for them to bake.
Over the past few weeks, we have eaten ALOT of cookies while testing this recipe.
These were ultimately the winning batch. These cookies are NOT crispy, but after polling you on Instagram over 85% of you said you prefer soft cookies!
These are in my opinion, ridiculously soft, totally gooey in the center, 100% delicious Paleo Pumpkin Chocolate Chip Cookies.

Substitutions for these Paleo Chocolate Chip Cookies
Honestly… I wouldn’t recommend any substitutions. As I mentioned earlier, I tried this recipe 8 times before perfecting it. I would just try to stick with the recipe if you can 🙂
Vegan Substitutions: I tried making these cookies without the egg and they were not as soft/chewy, and instead were a little more crumbly. I didn’t try these with a flax egg, but that might also be a good substitution. If you decide to try that – let me know.
Flour Substitutes: Almond and coconut flour are extremely finicky to bake with. I wouldn’t try to sub out either. If you’re looking for a nut free cookie recipe try this one. If you’re looking for a coconut flour free cookie try this one.
Sweetener Substitutes: I did not test this recipe with any other sweetener. I personally love baking with maple syrup and wouldn’t recommend that you change this part of the recipe. Honey may work, but I can’t guarantee it!
Chocolate Substitutes: Any chocolate will work in this. You can use chips, chunks, mini chips.. whatever you choose!

Now… the real question is… WHAT ARE YOU WAITING FOR?! Go bake these now!! Fair warning though, you might want to eat the whole batch in one sitting.. they’re very addictive!

Other healthy pumpkin recipes
If you’re looking for other delicious desserts, check out these Healthy Chocolate Chip Cookies

Paleo Pumpkin Chocolate Chip Cookies
Ingredients
- 1 tablespoon coconut oil melted + cooled
- ¼ cup pumpkin puree
- ⅓ cup maple syrup
- 1 egg whisked
- 1 cup almond flour
- 1/4 cup coconut flour
- 1 teaspoon cinnamon
- ½ teaspoon ground ginger
- ¼ teaspoon nutmeg
- 1/8 teaspoon cloves
- 1/4 teaspoon baking soda
- ½ teaspoon sea salt
- ½ cup dark chocolate chunks I use 80% coarsely chopped
Instructions
- Preheat oven to 350 and prepare a lined baking sheet with parchment paper or a silpat baking sheet.
- In a bowl whisk together coconut oil, pumpkin puree, maple syrup and an egg.
- Gently whisk in almond flour, coconut flour, spices and baking soda
- Fold in dark chocolate chunks to the batter
- Drop the dough in one tbsp balls onto the cookie sheet, pressing with your hands to flatten into small circles (about ⅓ inch thick. These cookies will not flatten on your own so be sure to press down before baking)
- Bake at 350 for 18-20 minutes until bottom of cookies are browned and start to get crispy on edges. Allow to cool for 10 minutes + enjoy!
Notes
- Vegan Substitutions: I tried making these cookies with out the egg and they were not as soft/chewy, and instead a little more crumbly. I didn’t try these with a flax egg, but that might also be a good substitution. If you decide to try that – let me know.
- Flour Substitutes: Almond and coconut flour are extremely finicky to bake with. I wouldn’t try to sub out either. If you’re looking for a nut free cookie recipe try this one. If you’re looking for a coconut flour free cookie try this one.
- Sweetener Substitutes: I did not test this recipe with any other sweetener. I personally love baking with maple syrup and wouldn’t recommend that you change this part of the recipe. Honey may work, but I can’t guarantee it!
- Chocolate Substitutes: Any chocolate will work in this. You can use chips, chunks, mini chips.. whatever you choose!
- WW Freestyle note: Points calculated using Lily’s Dark Chocolate Baking Chips. Save 1SP per serving by using sugar free maple syrup.
Joe says
It’s hard to find paleo dessert recipes that actually turn out good and don’t have a ton of random ingredients. These were a great way to use up leftover pumpkin puree that I had!
The Clean Eating Couple says
Glad you liked them, Joe! I wanted them to be pretty easy with minimal ingredients 🙂
Alyssa says
I’ve made these a few times now and I am always impressed with them. Delicious and healthy!!
The Clean Eating Couple says
Thank you so much, Alyssa! So glad you like them!
Sara says
Made these last night and my fiancé and I thought they were so delicious! I have more pumpkin to use up, so I will be making again! Thanks for the recipe!
The Clean Eating Couple says
So glad you both enjoyed them! Thanks, Sara!