Pumpkin Seed Chocolate Chip Cookies

by Maggie on February 29, 2012

I have a new favorite flour – pumpkin seed flour.  I’ve been experimenting with it for a month or so now and I just can’t get enough!  Oh, and you won’t believe how well it pairs with maple syrup – it just happens to be maple syrup season in these parts!

There’s so much to love about pumpkin seed flour:

  • I can make it at home with my coffee grinder;
  • Pumpkin seeds are high in iron and zinc;
  • Pumpkin seed flour is a nut-free replacement for almond flour;
  • They add incredible flavor to your baked goods.

I’m always playing with cookie recipes and this recipe for Pumpkin Seed Chocolate Chip Cookies was born out of a desire for a healthy, high-protein treat.   You could easily omit the chocolate chips and use carob chips or raisins instead.  Regardless, I know you’ll love these cookies.

What I love most about pumpkin seed flour is the nut-free factor.  We don’t have any nut allergies in our family, but I know a lot of people who do, plus these are a safe school lunchbox snack. In addition, pumpkin seed flour is perfect for those of you who like your sweets, but want to get some nutritional value at the same time.

Guilt-free, right?  And isn’t that why we love using almond flour in our baking?

Pumpkin Seed Chocolate Chip Cookies

1 ½ cups pumpkin seed flour (I use raw pumpkin seeds to make my flour)
½ cup ground flax seeds
½ cup ground quinoa flakes
1 teaspoon baking powder
1/2 teaspoon sea salt
1 teaspoon vanilla
1/3 cup maple syrup
1 tablespoon psyllium husks
1/3 cup coconut oil, melted
1/2 cup Enjoy Life Chocolate Chips

1. Preheat oven to 350 degrees. Prepare a baking tray.
2. Grind pumpkin seeds, flax seeds, and quinoa flakes separately (I use a coffee grinder).
3. Combine ground pumpkin seed flour, ground flax seeds, ground quinoa flakes, baking powder, and sea salt in a large bowl.
4. In a smaller bowl mix vanilla, maple syrup, and psyllium husks.  Let sit for a few minutes as it thickens.
5. Stir in melted coconut oil (I melt mine in a oven-safe glass dish while the oven is preheating).
6. Add wet ingredients to dry ingredients and mix well.
7. Stir in chocolate chips.
8. Scoop dough onto the prepared baking sheet.  Press gently with hand.  Bake at 350 degrees for 10-12 minutes. 9. Remove from the oven and let cool on the tray for 5 minutes. Move to a cooling rack and let cool completely.

Store in an air-tight container.

Yield: 24 small but powerful cookies


  • I buy psyllium husks at our local health food store.  Psyllium is an excellent source of fiber and a great replacement for xanthan or guar gums.
  • If you don’t have a sensitivity to oats, you can use gluten-free oat flour instead of ground quinoa flakes.
  • Grind the pumpkin seeds, flax seeds, and quinoa flakes separately so your measurements are correct.

The winner of last week’s Spunky Coconut giveaway is Jessica – here’s her comment: “Those muffins look amazing, as do the bagels. Can’t wait to try them! Thanks for doing this giveaway. :)”

If you didn’t win a copy of the book, you can buy it on Amazon, or at least put it on your wishlist!

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{ 28 comments… read them below or add one }

Zoe February 29, 2012 at 10:24 am

These look great, Maggie! Pumpkin and maple syrup, mm… :) My family loves maple syrup. Have you ever tried maple syrup on snow? It’s kind of fun.


Amber February 29, 2012 at 11:22 am

WOW! These look amazing Maggie. Great recipe. I will have to check out that pumpkin seed flour. It’s a SCD friendly food, so I’m sure it will make its way into my kitchen. :-)



Jen February 29, 2012 at 11:33 am

Thank you for this delicious recipe! I had a bag of pumpkin seeds in my kitchen just begging to be used. The raw batter is to die for, very satisfying.


Cassidy February 29, 2012 at 12:05 pm

Wow! These look great! I’ve never heard of pumpkin seed flour but you make it sound so great I will definitely have to try it. Thanks for the great recipe :)


Andrea February 29, 2012 at 12:28 pm

Fancy that! I’ve never thought of using pumpkin seeds as a flour! I’ll definitely have to try this.


Alta February 29, 2012 at 1:27 pm

Love these! They sound so tasty. I adore pumpkin seeds. Do you use the green ones? Cause the cookies don’t look greenish – so wondering!


Laura @ Gluten Free Pantry February 29, 2012 at 3:21 pm

Wow-pumpkin seed flour. Awesome! I need to try that and make these yummy cookies :)


Linda Lawrence February 29, 2012 at 3:59 pm

These sound awesome. I might just have to pick up some pumpkin seeds and see what I can do. We have lots of local maple syrup happening now too so that sounds like a great combo. Thanks Maggie.


Annie February 29, 2012 at 5:53 pm

My goodness these look good! They are super close to being ACD friendly too….do you have any tips for trading stevia for maple syrup? I know this sounds kind of far fetched but do you think it could work if I sweetened 1/3 cup of apple sauce with stevia in place of the maple syrup? (Can you tell how desperate I am for a cookie!?!) Also, just wondering if sunflower seeds could also work as a flour? I’ve never thought of using seeds as flours before…


Cara February 29, 2012 at 6:31 pm

I was about to ask where I can buy pumpkinseed flour, but I see the more appropriate question is, “where do I get a bigger coffee grinder?” because I’m gonna need a bigger one!


Alison February 29, 2012 at 6:46 pm

I haven’t yet tried psyllium husks in my gf baking….after being sick for so many years i’ve been afraid of the fiber. lol! But your cookies look great and I’ll definitely be giving them a go now that my gut has healed a bit.


StoriesAndSweetPotatoes February 29, 2012 at 7:10 pm

I love discovering new flours and this is a new one for me! What brand is it?


Kim - Cook It Allergy Free February 29, 2012 at 8:06 pm

So these look down right amazing. I want to make these right now…but first I need some raw pumpkin seeds. Here is my question: Have you found that you can sub an equal amount of pumpkin seed flour for almond flour? THat would be amazing if so, because I have so many almond flour recipes that I hesitate to post on my blog because of all of my followers that have nut allergies.
Love this one, Maggie!!


Heather J February 29, 2012 at 8:37 pm

I made these and they are delicious! I made the flour in my food processor (using 1/2 cup sunflower seeds and 1 cup pumpkin seeds to make 1-3/4 c seeds flour total) so the dough was crumbly. However the cookies baked up just fine. Thanks for the recipe!


Alisa March 1, 2012 at 11:08 am

Brilliant recipe Maggie! I love grinding nuts and seeds into flours, but hadn’t tried pumpkin seed yet! And maple with chocolate … mmmmm.


Carol March 1, 2012 at 1:11 pm

mmm, pumkin and maple is a match made in heaven! What a genius you are with your pumpkin seed flour!


Shirley @ gfe March 3, 2012 at 10:08 am

Oh, Maggie, these cookies look and sound so good, and good for you, too! :-) Off to share …



Nancy @Real Food Allergy Free March 3, 2012 at 5:04 pm

This is brilliant! I just shared these on facebook. I can’t wait to experiment with pumpkin seed flour and try these. Please, please, please share these at Allergy Free Wednesday! http://www.realfoodallergyfree.com/2012/02/allergy-free-wednesday-229/


Sarah March 3, 2012 at 7:37 pm

These look amazing! I need to get more healthy foods into my 18 month old. I think he will love them. Do you think I can use quinoa flour instead of ground quinoa flakes? Thanks!


amelia May 4, 2012 at 12:17 pm

I don’t even want to know the caloric value in these. I just ran 3 miles and whipped these cookies up for the first time. I will have to run another 3, because I am going to eat the whole batch! Thanks for sharing! Cheers!


Susan February 12, 2013 at 7:41 pm

Hi there,
I literally Googled ‘ground pumpkin seed cookies’ and found you! And also thought choc chips would be good! Now I don’t have to invent my own version–/ all for the same reasons (nutfree but protein!). They are for my son who has autism. Would you believe he is sensitive to quinoa, flax, and psyllium? Do you think I can use ground chia seeds instead of the psyllium (and for the flax, too)? Will use our GF oats ground into flour instead of quinoa.


Susan March 9, 2013 at 7:34 am

Turned out great without the psyllium – used an egg instead, actually. AND, threw in 2 tbsp. cocoa powder! Yum.


Cheryl Caplan April 2, 2013 at 9:08 pm

These are my absolutely most favorite cookies ever! I’ve been gluten and dairy-free for nearly 10 years and was really missing a good cookie. These are so chock full of nutrition that I feel pretty virtuous while eating them. If only I could keep the rest of the family from devouring them too! Thanks for the recipe!!


Charu April 23, 2013 at 9:23 am

This is an awesome cookie recipe! Very creative! Thanks so much for posting this.

I didn’t have quinoa flakes so used quinoa flour and still came out good! My son has multiple food allergies and this cookie is great for him.


Oi August 6, 2013 at 5:03 pm

I’m guessing you didn’t use Pumpkin seeds with shell then huh?


Maryam April 16, 2014 at 7:07 pm

Hi there! I make these cookies all the time and use cocoa powder in the flour to make them chocolatey, they’re amazing! Just wondering if you’ve bee checked the caloric content per cookie out of curiosity? Thanks again!


Denise February 9, 2015 at 1:18 pm

Hi Maggie:
Thanks for this great recipe.
My DH was found to be low in phosphorus – so, I looked up phosphorus rich foods, found that pumpkin seeds were at the top of the list. Certainly he could just eat the seeds, but I wanted to see if there were any vegan muffin/cookie recipes using ground raw pumpkin seeds and my search led me to you : ) <3
Your blog is awesome – I've bookmarked it.
Thanks again : )
Many blessings to you and yours,


Elsa February 20, 2016 at 12:23 am

Seriously impressed with this recipe! Thank you for sharing! Will be making this a lot from now on – great GF DF wholesome fuel for long bike rides :)


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