Healthy Chocolate Crinkle Cookies (Protein Packed)
These Chocolate Crinkle Cookies are easily one of my favorite recipes ever.
I know, that’s very high praise. But if you make this recipe, you’ll see exactly why I love it so much.

These healthy chocolate crinkle cookies are essentially soft, decadent brownies in cookie form.
They’re soft and moist inside, and yet the outside has a slight crisp to them. If you like brownies with crackly tops (who doesn’t?) then you’re going to LOVE these chocolate crinkle cookies.
Each of these cookies is only 85 calories, contains 5g of protein, and is completely gluten-free!

I’ve made these healthy crinkle cookies for the past few years now, and it’s the one recipe I most look forward to during the Christmas season.
How to make healthy chocolate crinkle cookies
Since we’re making a chocolate crinkle cookie with a healthy twist, the way we prepare it is a bit different than traditional crinkle cookies.
We’re going to mix up a pretty straightforward cookie dough for this healthy recipe, with the two key ingredients (aside from the protein powder) being dark chocolate and peanut butter.
When melted together, they create a smooth and creamy fat source that is necessary for these cookies.
If you have a peanut allergy, any nut butter will work in its place, but the peanut butter will give us the best bang for our buck in terms of protein. I more recently tried these cookies with almond butter, and since it’s a much more subtle flavor than peanut butter, you may prefer to go that route to really let the chocolate flavor shine.

To make the chocolate cookie dough, add all of the dry ingredients to a bowl: almond or oat flour, protein powder, cocoa powder, brown sugar, and baking soda (NOT baking powder).
Then we’ll add the melted chocolate mixture along with some unsweetened applesauce, which helps add moisture with very few calories, and mix together into cookie dough.
Once you’ve mixed up your cookie dough, you’ll have to let it chill in the fridge for one hour.

Since the “crinkle” effect is so important for these cookies, chilling is essential. Chilling the dough prevents the cookies from spreading too much, allowing us to create that crackly effect after they are baked.
If you skip the chilling process, your cookies will spread thinner and you won’t achieve the same crinkle effect.
Once the dough has chilled, we’re going to roll 8 cookie dough balls and generously coat them in powdered sugar substitute (or regular powdered sugar).

These cookie dough balls should look just like Chocolate Donut Holes at this point (and you can technically eat them at this point if you truly can’t help yourself since the chocolate cookie dough is safe to eat raw).
Bake the cookies at 350 degrees F for 8 minutes.
When the cookies come out of the oven, they’re going to look very puffy and cakey…

Don’t worry, this is perfectly normal.
While the cookies are still warm and soft, using your hands (or a spatula) to gently press down the tops of the chocolate cookies to create that crinkle effect.

Don’t squish the cookies completely flat, because we still want there to be a soft & gooey interior to them. Just a little bit of pressure is all you need to press the tops of these chocolate crinkle cookies down.
Allow the cookies to cool for roughly 10 minutes to firm up inside, then they are ready to be enjoyed.

If you have leftovers, you can keep these cookies stored in an airtight container at room temperature for up to one week.
I’ve found that if left uncovered, the exterior retains a slight crisp, but you run the risk of the cookies drying out. When stored in an airtight container, the cookies will become a bit softer, but they will remain fresh for days.

More chocolate recipes to enjoy
Ready to get chocolate wasted? While these chocolate crinkle cookies are truly my favorite chocolate recipe on the blog, I have plenty more chocolatey recipes to satisfy your cravings. Here are some of my favorites that are worth checking out:
- Half Pound Chocolate Protein Cookie with 50g Protein
- Easy Chocolate Fudge
- Low-Calorie Fudgsicles
- Healthier Chocolate Donut Holes
- The BEST Protein Brownies
Healthy Chocolate Crinkle Cookies (Protein Packed)
These healthy chocolate crackle cookies will change the way you look at Christmas cookies! If you love chocolate, this will definitely become your new favorite Christmas cookie.
Ingredients
- 33g (1 Scoop) PEScience Chocolate Truffle Protein (or another chocolate whey/casein blend protein)
- 30g Almond Flour or Oat Flour (See Notes)
- 10g Unsweetened Cocoa Powder
- 30g Brown Sugar Substitute (or regular brown sugar)
- 32g (2 Tbsp) Nut Butter of Choice
- 50g Unsweetened Applesauce
- 45g Dark Chocolate (melted)
- 1 tsp Baking Soda
- Pinch of salt
- Powdered Sugar Substitute for Coating
Instructions
- Add the nut butter and dark chocolate to a small bowl and microwave for about 30 seconds until melted and smooth.
- Add all of the dry ingredients together in a large bowl, then add the melted chocolate mixture and applesauce to the same bowl and mix until cookie dough forms.
- Refrigerate the dough for one hour to firm up. Chilling the dough helps prevent the cookies from spreading too thin during the baking process.
- After the dough has chilled, preheat your oven to 350 degrees F.
- Break off small pieces of the dough and roll them into balls before placing them on a cookie sheet. I made 8 cookies out of my dough, but you can make more or less depending on the size you would like.
- Roll each dough ball in powdered sugar to completely coat, then bake for 8 minutes.
- Remove the cookies from the oven and immediately press the cookies down with your fingers or a spatula to flatten them and create the crinkle effect.
- Let the cookies cool for about 10 minutes to firm up inside, then enjoy!
Notes
- PEScience Chocolate Truffle protein made the BEST version of these cookies, but I have also used the vanilla flavor for a solid result. That obviously leads to a less rich chocolate flavor, but it still works great.
- The protein powder I use (PEScience) is a blend of whey & casein protein. In my experience, this works best for cookies. You can likely use 100% whey, but the resulting cookie may be dry. You can check out my protein powder substitution guide here, and you can save 10% on PEScience protein using the code "Matt"
- I originally made these cookies with oat flour, which is my preferred flour for cookies, but recently tried almond flour as well. The texture ends up virtually the same, so it comes down to a matter of preference. Almond flour will make these cookies carb-free, but also slightly higher in calories and fat.
- Peanut butter and almond butter have both worked really well in these cookies, but since peanut butter has a stronger flavor, it does come through a bit. If you want these cookies to taste exclusively of chocolate, opt for almond butter.
- I don't count the sugar substitute in my carb totals, so be sure to include those in your calculations if you are very strict about carbs.
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Nutrition Information
Yield 8 Serving Size 1 Crinkle CookieAmount Per Serving Calories 85Total Fat 4gCarbohydrates 9gProtein 5g

I’m making these tomorrow with the new PEScience Chocolate Truffle and I’m so excited! I do have a silly question though, after I take them out of the often do I leave them on the baking sheet to cool or transfer them to a cooling rack? Sorry I know it’s a dumb question, I am new to baking with protein powder and I just don’t want to mess them up!
I have these on my list to re-make very soon with that protein as well!! And that’s not a silly question at all. I let them cool right on the baking sheet. They’ll be a little delicate while hot so it’s much easier than trying to transfer them!
@Matt, okay that’s exactly what I did! But oh my gosh they just came out of the oven about 20 minutes ago and I may have already had two (oops), they are SO delicious especially with the chocolate truffle!! You have to remake soon seriously I am obsessed. Thank you so much for this recipe, you never miss!
I can’t wait to make this! Do you think whole wheat flour can be used instead of oat flour?
@Kara, It might make these a little more “cakey” but I would guess that it will mostly work!
@Matt Rosenman, gotcha, I will just blend some oats! Thank you so much for this!