These whole grain Spelt Chocolate Chip Cookies are a clean eating dessert made with coconut oil and unrefined sugar. They are a delicious way to satisfy sweet cravings with wholesome ingredients.

When it comes to dessert or sweet treats, cookies are definitely my favorite kind. I love how simple and quick they are to make (aside from sometimes torturous chilling times). They are sweet with lots of different textures. And you can have them with added ingredients to your hearts desire - chocolate, nuts, candy, dried fruit, oatmeal...
Really - what's not to love about cookies?
While oatmeal cookies may be my personal favorite, chocolate chip cookies are a timeless classic. I like them best with crisp edges and chewy centers. I already made a spelt flour double chocolate chip cookie before, but now it is time for the true classic.


My sister brought me organic whole grain spelt flour from Oak Manor from Canada when she visited us over the holidays. I've loved experimenting with this stone-ground ancient grain from a Canadian producer.
I've mainly been using it in hearty homemade breads, but then I had the idea to make spelt cookies - chocolate chip cookies to be exact. I used coconut oil, coconut sugar (or unrefined cane sugar), Oak Manor spelt flour and dark chocolate chips to make these clean eating chocolate chip cookies.
The spelt flour cookies turned out super delicious! Compared to regular cookies made with white flour this spelt cookie recipe produces a little heartier texture and slightly nutty flavor. And with chewy centers and crisp edges these healthy spelt cookies turned out just the way I like 'em.
If you are looking for a more filling, protein-rich cookie option I recommend Naked Chocolate Chip Protein Cookies. Each cookie has 10g of protein and only 1g sugar. They are gluten free, soy and GMO free and don't use high fructose corn syrup or artificial sweeteners.

When making these spelt flour chocolate chip cookies, don't skip the step of chilling the dough balls. I choose to make these spelt cookies with coconut oil that has been melted, so the chilling just helps them to retain their shape.
I've tried skipping it and ended up with chocolate chip spelt cookies that spread so much that I basically ended up with a sheet of cookie. I assure you we still ate it all; this way the cookies with spelt flour just didn't look very presentable.
To achieve the chewy centers that I like so much, I slightly underbake these clean chocolate chip cookies - like all my other cookie recipes.
I take them out of the oven when the edges are set but the centers can still look glossy. They still keep on baking on the hot cookie sheet outside of the oven, but they won't overbake.
Keep the cookies in an airtight container to ensure they keep their crisp edges.
More Chocolate Chip Cookie Recipes:
- Coconut Flour Cookies - these are paleo, gluten free with a low-carb/keto option
- Tigernut Flour Cookies
- Double Chocolate Chip Spelt Cookies
- Gluten Free Oat Flour Chocolate Chip Cookies

Clean Eating Spelt Chocolate Chip Cookies
Ingredients
- ¾ cup coconut sugar or unrefined cane sugar
- ½ cup coconut oil melted
- 1 egg
- 1-½ teaspoons vanilla extract
- 1-½ cups spelt flour
- 1 teaspoon baking soda
- ¼ teaspoon salt
- ¾ cup dark chocolate chips
Instructions
- Stir together coconut sugar and melted coconut oil. Let sit for a few minutes to allow the coconut sugar to dissolve.
- Add the egg and vanilla extract and stir (by hand or with a mixer) until combined.
- Add spelt flour, baking soda, and salt and stir together until just combined. Fold in chocolate chips by hand.
- Using a large cookie scoop form about 12-14 dough balls. Press a few more chocolate chips into the top of each dough ball. Cover with plastic wrap and refrigerate the dough balls for at least 1-2 hours (or ½ hour in the freezer).
- Preheat oven to 350 F and place chilled dough balls 2 inches apart on a parchment or silicone lined baking sheet.
- Bake for 8-10 minutes until the edges are just set. Centers can still look slightly uncooked. Let the cookies cool on the baking sheet for about 10 minutes, then move them to wire rack to cool fully. Store airtight.
Nutrition
Products used in this Spelt flour cookie recipe:
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Amy
Fantastic recipe! Thank you ! They came out perfect. I was nervous at first as the dough was very "wet' but they cooked great. Delicous cookies. I cant wait to play around with this receipe. I used regular white sugar as I was anxious to try these and had no other sugar. I love them. =)
Jennifer @ Leelalicious
Thanks for your review, Amy! I'm so glad you love them!
H. Proude
Terrible. Wasted my organic baking ingredients.
Jennifer @ Leelalicious
I'm sorry you didn't enjoy this recipe! Let us know if you had any specific issues with the recipe.
Lindsay M
These are so delightful! I've made them 3 days in a row. I used Spectrum palm shortening instead of coconut oil. Yesterday and today, I added about 1tbsp of chia seeds. So delish!
Jennifer @ Leelalicious
Thanks for your lovely review, Lindsay! The chia seeds sound like a great addition.
Laura
Oh my goodness. The best cookie recipe ever! So excited. It tasted delicious and will be making them on the regular! I ran out of baking soda so replaced with 3 teaspoons of baking powder
Jennifer @ Leelalicious
Thanks for your lovely comments, Laura! 🙂
Ipsa
These are so quick and easy to make. And so delicious. Thank you for the recipe
Jennifer @ Leelalicious
Thank you for the lovely comment, Ipsa! I'm so glad you enjoyed these.
Shivi
So, I followed the recipe exactly as it was written (only substituting Coconut sugar with regular sugar instead), but ended up with an extremely soft dough which was too light to hold shape. I couldn't even roll the balls of dough to freeze before baking, because while I was rolling one, the others already spread into a flat splash. I resorted to chilling the entire dough in the freezer for about an hour and only then formed the balls which seemed to work much better. However, after chilling (again in the freezer) the now rolled cookie balls - they again came out of the freezer almost entirely flat. Nevertheless - I went ahead with the baking, being very skeptical as for the end result. However - to my big surprise - the cookies came out perfect! They were a bit too big and flat to my taste, but still - deliciously flavored, and perfectly textured, with a nice crisp outside and a chewy moist inside. I was super careful with the baking times and temperature, so to not overbake, literally watching them as they bake. While ovens vary, mine took 8 minutes sharp.
Overall, thanks for a surprisingly great recipe, for great cookies that got great compliments from all. I will definitely make them again, and again.
Jennifer @ Leelalicious
Hi Shivi, thank you for your lovely comment! I'm glad that the recipe worked out for you after all.
Katie
Ok…. So I look for recipes and land on this one… it looks easy, fast, and made with ingredients I always have on hand. As I am assembling the cookies and get to the chocolate chip part, I realize that my inventory taking skills need honing…. No choc chips… Instead I used toasted pumpkin seeds and sesame seeds…. Didn’t change anything else… FYI, this recipe is great with toasted seeds! Might even toss in some shredded coconut next time… Thank you for this recipe…It’s a keeper and so versatile. Cheers!
Jennifer @ Leelalicious
Hi Katie, I love those ideas! I can imagine how much toasted flavour and texture those seeds must have added! 🙂
Carol
Is it white or wholemeal spelt flour please
Jennifer @ Leelalicious
Hi Carol, it should be wholemeal spelt flour. Happy baking! 🙂
Janet
Used the basic cookie recipe, but added 1 t. Cinnamon (mixed into the flour mixture) and then substituted 2 c. chopped pecans for chocolate chips. Turned out delicious!
Regina | Leelalicious
Cinnamon and chopped pecans sound like fantastic additions for this recipe. Thanks for sharing this great idea
Lani
I don’t have coconut sugar on hand,
Would maple syrup or honey work as a substitute?
Regina | Leelalicious
Liquid sweetener makes for a very different cookie texture. It works (use about 1/2 of the granulated amount) but the cookies will be soft and slightly chewy. Not crispy
Sheesha
Hi... I’m a novice baker on the lookout for easy recipes. I’m going to try this as it looks very promising. I have a very basic q? - but what is the best rack to bake cookies on?
Regina | Leelalicious
Always in the center
Devorah
Super delicious. Thank you!
Nivi
Hello Regina,
I tried the recipe to the T and it came out delicious.
If I want to substitute coconut oil with butter, how much butter should I be using?
Regina | Leelalicious
Great to hear. I would use an equal amount of butter
Catherine Bricca
Excellent recipe, perfect cookies every time! I’ve made these probably 20 times already, to bring to parties as well. I just replace the coconut oil with almond oil. Thank you!!!
Laurissa
These have become our favourite iso cookies! I’ve just made my third double batch for the week!! We’re not DF or vegan, so I substituted the coconut oil for butter (but cut back to 200g for the double batch). We’re also using half a block of chocolate shaved / chopped for double batches, which is enough chocolate for us 😉 Thanks for a great recipe!
Natasha
These are our new favourite recipe. I make a double batch but they still don’t last long. I suspect we have gremlins 😉
Courtney
These are our all time favorite cookies!! I have been really trying to get the perfect tasting chocolate chip cookie with spelt flour, coconut sugar and we use a flax egg instead of a real egg and the recipe turned out perfect!! Thank you!!!! I will make these forever!
Dalia
Hi Regina, thank you for this recipe. I have doubled it and the texture is great however the taste was bitter. Is it due to the coconut sugar? Thanks so much, Dalia
Regina | Leelalicious
Hmm.. I have never noticed a bitter flavor with coconut sugar, but maybe your brand had a more prominent burnt caramel flavor to it? I have also heard that some are more sensitive to the bitterness of baking soda. Maybe try using about twice the amount of baking powder instead next time
Charlotte
Hi I am in the uk please could I get the measurements in grams? 🙂 thanks
Regina | Leelalicious
Hi Charlotte, I've just added metric measurements to the recipe. Be sure to select to "Metric" below the ingredient list to switch.
Nivi
Hello Regina - thank you for sharing this wonderful recipe.
Baked my first ever chocolate chip cookies.
This is a simple yet great recipe. I followed the recipe to the T and it came out delicious. And exactly the texture I wanted.
I put the scooped dough balls in the freezer for 25 mins and it came out perfect!
Cheers,
Nivi