These delicious pumpkin seed flour chocolate chip cookies are made with oats and pumpkin seeds, making them a great nut-free and gluten-free alternative for those with allergies!

For a while now, I've wanted to make a chocolate chip cookie with pumpkin seed flour.
Pumpkin seeds, ground into flour with a food processor or Nutribullet, make a great replacement for almond flour.
I also enjoy that the seeds add good amounts of zinc and protein to the recipe.
Pumpkin seeds are also low in oxalates. All you have to do to make the flour is grind raw pumpkin seeds down to a meal consistency and add them to recipes like these Whoopie Pies.
This recipe is not only gluten-free, it's also egg-free and nut-free. The only tic I'm missing is 'grain-free', and if that's what you desire, you might try this popular cookie recipe.
Ingredients and substitutions

- Flour - As I wrote above, I use a combination of oat and pumpkin seed flours. Almond flour would be a suitable substitute for pumpkin seed flour.
- Baking powder AND baking soda - Both leavening agents are used to create a golden cookie.
- Sea salt, vanilla extract - Both provide flavor to the cookies.
- Butter or coconut oil - Be sure you're using it in a softened state, not melted. Using coconut oil will keep them dairy-free.
- Coconut sugar - Any granulated sugar will work.
- Applesauce - This adds both sweetness and texture. It can be replaced with more softened coconut oil or butter, but that obviously adds more fat.
- Water - Warmed water helps the batter to mix together.
- Stevia - This is a source of sweetness for the recipe. If you don't like stevia, monk fruit could be used or you can up the sugar to 1/2 cup.
- Chocolate - I love using chopped chocolate in my recipes, as it's more economical.
How to make pumpkin seed flour cookies
Stir together all of the dry ingredients in a large bowl and all of the wet ingredients in a separate, smaller bowl.
Mix everything together, including the chocolate. You can reserve some chocolate for the tops as well.


Drop the batter by the spoonful onto a baking sheet. The recipe makes 12 good-sized cookies.

Be sure to let these cookies sit for a bit after coming out of the oven. Because there isn't a common binder like gluten or eggs, these are a bit more fragile.

Recipe tips
This post tells you exactly how to make Pumpkin Seed Flour.
The butter or oil should be in a soft state, not melted, and not solid either.
If you prefer to avoid stevia, you can omit it and use either 1/2 cup TOTAL granulated sugar OR substitute two tablespoons of maple syrup for the two tablespoons of water.
More pumpkin seed flour recipes
Fudgy Pumpkin Seed Flour Brownies
Pumpkin Seed Flour Cookie Dough Bites
The kids ate up my whole batch in one afternoon, prompting Jade to inquire, 'mommy, why didn't you make more??'. A good sign, I'd wager!
Pumpkin Seed Flour Chocolate Chip Cookies
Ingredients
- 1 cup oat flour
- 1 cup pumpkin seed flour
- ½ tsp baking powder
- ½ tsp baking soda
- ½ tsp sea salt
- ¼ cup softened coconut oil or butter
- ¼ cup coconut sugar
- 2 teaspoons vanilla extract
- 2 Tablespoons applesauce
- 2 Tablespoons warm water
- 15-20 drops liquid stevia
- ¼ cup chopped chocolate or chocolate chips
Instructions
- Preheat the oven to 350 degrees, and begin with room temperature ingredients.
- Mix the dry ingredients in a large bowl (flours, baking powder, baking soda, and salt).
- In a separate smaller bowl, whisk together the butter or oil and sugar until well combined. Then, whisk in the vanilla, applesauce, water, and stevia.
- Add the oil/sugar mixture, as well as the chocolate, to the dry mix and stir until a batter forms.
- Using a tablespoon, divide the batter into 12 and 'drop' the cookies onto a parchment paper-lined baking sheet.
- Bake for 8-10 minutes or until edges are golden.
- Let them sit for about 10 minutes to help them hold their shape.
Notes
Nutrition
If you have a chance to try this recipe, please leave a star rating and a comment below letting me know how you liked it!







Nancy
I have dry stevia extract that comes with a tiny scoop. Can I use a scoopful in place of liquid stevia extract?
Lauren
Yes, that should work fine!
Lynn
I would like to know what kind of pumpkin seeds to buy? Raw? Roasted? Unsalted?
Thank you.
Lynn M.
Lauren
Hi Lynn,
I use raw, unsalted seeds. 🙂
Lynn
I have one more question before I can make these.
I don't use Stevia.
How much regular sugar and/or brown sugar should I use instead of Stevia?
Or how of all coconut sugar should I use instead of Stevia?
Can I use regular sugar and brown sugar with coconut sugar?
Thank you so much. I'm having to relearn how to bake with all these new ingredients. 🙂
Lauren
Hi Lynn,
So, I would use 1/2 cup total coconut sugar if you leave out the stevia. To just use regular sugar, I would use 1/4 cup regular sugar with 1/4 cup of brown sugar, though that's more of a guess. Please let me know if you try them and how they come out! 🙂
Danielle
These were wonderful! Thank you for the easy sugar-free cookie. We can’t have coconut sugar so we substituted one Stevia In the Raw packet in addition to the liquid stevia and the result was great!
I omitted the chocolate chips and slathered some homemade green colored stevia and palm shortening to make a festive frosting for my son’s St. Patrick’s Day school party.
Thanks again, may be our new go-to!
Diana
Can I use ww pastry flour or all purpose flour instead of pumpkin seed flour? Thank you
Lauren
Hi Diana,
The pumpkin seed flour adds some fat, which adds moisture, so I think the recipe will be dry if you do that. I think this recipe would do well with pastry flour though: https://www.oatmealwithafork.com/barley-flour-cookies/
Diana
Thank you Lauren for the alternative recipe that uses barley flour instead.
Gina Little
I can't tell if these are chewy, cakes or crispy. Can you please describe?
R
These look great!