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Fudgy Chocolate Protein Cookies

What do you get when you cross protein cookies with brownies?

The gooiest, fudgiest, best chocolate protein cookies in the world.

Chocolate protein cookies

I wanted these chocolate protein cookies to have all of the amazing flavor and texture of a brownie wrapped up inside a delicious cookie.

If you like chocolate, you’re going to love these cookies. I promise.

This protein cookie recipe was first developed many years ago, but I decided to revisit it to make it even better. Through all of my recipes, I’ve learned a lot about high-protein baking, so I’ve been able to periodically go through and improve my older recipes.

Stack of chocolate protein cookies

My goal with these chocolate protein cookies was to create a recipe that could stand on its own as a delicious chocolate cookie, protein or not.

And I’m proud to say that is exactly what we have here.

With 135 calories and 8 grams of protein per cookie, these are the perfect snack to curb that sweet tooth of yours.



Main Ingredients & Substitutions

Healthier baking (especially high-protein baking) requires using pretty specific ingredients.

If you make substitutions without too much thought, you’ll often end up with a terrible result. I’ll break down some of the main ingredients in this recipe, along with some possible substitutions to help you make the best chocolate protein cookies possible.

Holding chocolate protein cookie

Main Protein Source: A Whey/Casein Blend.

Whey protein is typically the cheapest and easiest to find, and most people have some form of whey protein in their cabinet already.

That being said, I have found a combination of whey & casein protein to be the superior choice for baking, especially when it comes to cookies.

The understand the difference in powders, I like to use the “just add water” test. If you put some whey protein in a bowl, add a few tablespoons of water, and mix, you’re going to get a really sticky mixture. It’s not something you’d just want to eat by the spoonful.

But when it’s a whey/casein mixture (or 100% casein), it’ll mix up and be similar to pudding. The casein doesn’t absorb the same amount of liquid, so you get a much smoother result.

When used in baking, you end up with more moisture using whey/casein together. Whey protein on its own tends to dry out much quicker, so using the combination of whey & casein allows you to go lower fat while still retaining plenty of moisture.

Look at this example from my giant protein cookie recipe:

When I used whey protein, the cookie spread thinner and ended up being more dry.

I cannot recommend PEScience protein (a whey/casein blend) enough. If you plan on making any of my recipes on my site, PEScience is the protein you’ll want to grab to follow the recipes as closely as possible.

I’ve used Bowmar Nutrition’s whey protein powder in the past, and you can definitely use that (or another whey protein) in these cookies. However, be warned that the final result might be on the dry side. I haven’t done a direct test, but whey protein should still work for this recipe, albeit not as well.


Main Flour: Oat Flour

I’ve been loving baking with oat flour recently, and it’s my go-to for cookies. Not only does it lend a really authentic cookie flavor, but it’s gluten-free AND plays really nicely with protein in baking. You can very easily make your own by throwing some oats into a food processor or spice grinder.

If you need to swap oat flour out in this recipe, I like to use a combination of almond flour and coconut flour. Almond flour on its own won’t work great because it doesn’t bind very well, so the coconut flour really helps add structure.

You may be able to use all-purpose flour, but my fear is that it would create cookies that are cakier than we’d like.


Liquids: Butter, Peanut Butter & Applesauce

In my original version of this recipe, I used peanut butter and unsweetened applesauce as my liquids, then used a little bit of milk to add additional moisture to the cookie dough.

Since the original recipe, I have developed a ton of cookie recipes, and I’ve learned that it truly is a science. And, there’s a reason why most cookies call for butter- it works the best!

So, in my new & improved version of this recipe, I’ve also included butter in this recipe.

Butter & peanut butter combine to be our fat sources in this recipe, which help to create a very soft cookie with the perfect amount of chew.

Chocolate Protein Cookies

If you want to achieve this perfect texture, you don’t want to skip the fat. Don’t worry, you won’t taste the peanut butter much at all.

If you can’t do peanut butter, any nut butter will work in place, or you can bump up the amount of regular butter (the downside to that is that you’ll be eliminating some protein).

Applesauce is a secret ingredient in baking that mimics eggs without adding any extra fat. To help keep the calories on the lower side, I love using unsweetened applesauce in place of eggs or oil. This is a necessary ingredient to keep these cookies moist and gooey!

You should be able to use some milk instead of applesauce if you don’t have any, though.



How to Make Chocolate Protein Cookies

Making these chocolate protein cookies is fairly straightforward, but I’d like to help clarify a few important steps for you.

The process for making our cookie dough is simple: mix up all the dry ingredients in a bowl, then melt the chocolate chips, butter, and peanut butter together before adding that to the dry ingredients.

Once you add those liquids along with some applesauce, it will come together to form chocolate cookie dough.

At this point, we have to let the cookie dough chill for one hour.

I know that waiting is terrible, but if you were to bake these chocolate protein cookies right away, you would not achieve the same fudgy and gooey texture.

Chocolate cookies on baking sheet

Once the dough has chilled, you’ll break it up into 6 pieces, then press each down into a hockey puck shape.

We don’t need to completely flatten these into cookie shapes, but slightly flattening the tops helps these chocolate protein cookies to spread to be the size we are after.

Bake these cookies for 8 minutes, then remove them from the oven and allow them to fully cool.

When your cookies come out of the oven, they may not look as good as you are expecting. We’re going to do two very simple things…

Chocolate cookies after cooling

1. Use a cup to form your cookies into perfect circles while they’re still warm.

If your cookies aren’t a perfect circle, you can flip a cup upside down to cover the cookie, then quickly move the cup in a circular motion to slide the cookie around and form it into a circle.

Since the cookies are still warm and super soft, they’ll take shape very easily. Check the before and after photos above to see the difference.

2. Allow these cookies to fully cool before eating. These chocolate protein cookies will sink and set as they cool, so it’s important to give them time to rest.

I prefer to let my protein cookies sit for one hour before diving in.

Again, I know that waiting is terrible, but I promise you that it will be worth the wait!

Chocolate protein cookies

You can keep any leftover protein cookies stored in an airtight container and enjoy ’em throughout the week.


More Protein Cookie Recipes to Enjoy

Cookies are my favorite dessert to make, which means I have a ton of high-protein cookie recipes here on my site.

While I could never pick a favorite, here are some amazing ones to get you started:

CHocolate Protein Cookies

Stack of chocolate protein cookies

Fudgy Chocolate Protein Cookies

Yield: 6 Cookies
Prep Time: 10 minutes
Cook Time: 8 minutes
Inactive Time: 2 hours
Total Time: 2 hours 18 minutes

These chocolate protein cookies are packed with so much chocolately flavor that nobody would ever know that they were secretly packed with protein. And with only 135 calories each, these make a great option for curb any sweet tooth.



  1. In a large bowl, mix together all of the dry ingredients for your chocolate protein cookies (protein powder, cocoa powder, oat flour. brown sugar, baking soda, and salt).
  2. In a small microwave-safe bowl, add the butter, peanut butter, and chocolate chips. Microwave for 30 seconds and stir well to create a smooth mixture that you can add directly to your dry ingredients.
  3. Lastly, add the applesauce to your bowl and mix everything up with a silicone spatula until cookie dough forms.
  4. Refrigerate the chocolate cookie dough for one hour to allow the dough to firm up.
  5. After the cookie dough has chilled, preheat your oven to 350 degrees F.
  6. Break the cookie dough up into 6 pieces, roll them into balls, then place them on a parchment paper-lined baking sheet.
  7. Use your hands to slightly press the tops of the cookies down to create hockey puck shapes (see photos above this recipe card for reference). You do not have to completely flatten these into cookie shapes, but pressing the tops down will help these cookies take shape as they bake.
  8. Bake the cookies for 8 minutes.
  9. If you want these cookies to be perfect circles, you can place a cup upside down over each cookie and quickly move the cup in a circular motion to shape them into perfect circles while still warm.
  10. Allow these cookies to completely cool before eating. These chocolate protein cookies firm up as they cool, so proper cooling time is crucial (I typically let them sit for one hour).
  11. Store leftovers in an airtight container and enjoy throughout the week.


  • The protein powder I use is a blend of whey & casein, and I highly recommend using the same. I cannot guarantee results with other types of protein powder.
  • If you want to make these cookies lower in calories, you can swap the butter out for a light butter alternative. The final texture isn't quite as good as this version, but it still works great.
  • Even though these are chocolate protein cookies, you can also use vanilla protein powder if that is all you have. Since we're adding cocoa powder, vanilla still works.
  • This recipe is safe to eat raw, so no harm in underbaking if you prefer that! 8 minutes was the perfect amount of time to accomplish a nice soft cookie, though.
  • I don’t count sugar substitutes in my macros since they do not contribute to the overall calories. If you are super strict about carbs, make sure you take the sugar alcohols (depending on which sugar substitute you use) into account.

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Nutrition Information
Yield 6 Serving Size 1 Cookie
Amount Per Serving Calories 135Total Fat 8gCarbohydrates 9gFiber 2gSugar 3gProtein 8g

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Sunday 25th of February 2024

I have no applesauce—can I use banana?

Matt Rosenman

Sunday 25th of February 2024

Potentially, but that adds a pretty strong flavor. I might try using a small amount of milk in its place instead. Since it's the final ingredient, just add a small amount at a time to make sure you don't add too much- you want just enough to bring it all together.

Brooke D

Sunday 30th of July 2023

Love this recipe! I made it with PEScience’s vegan chocolate protein and just added a little extra applesauce so it wasn’t so dry. Great recipe, thank you!


Wednesday 26th of July 2023

So good 👍🏻


Friday 12th of August 2022

I’ve made this recipe three times. The first time they came out great.. moist and chocolately from the chips in the middle. The second time the cookies were much more dry and not as good. What I realized is the first time I used baking powder instead of the baking soda as the recipe intended. The third time I tried again with baking powder and they were moist again. Not sure the technical reason for baking soda but I recommend the same amount but of baking powder! Also I used the same protein powder as recommended (PEScience).


Monday 8th of August 2022

Hi I try it today with whey protein powder and it puffed up,also looking not so yummy But when I under bake it turns out perfect! Do you have any tips for using whey protein but also looking good tsk a lot

About Matt Rosenman

With over 15 years of experience in health and fitness, Matt Rosenman is the expert voice behind Matt’s philosophy is simple: no foods are off-limits, and a healthy lifestyle shouldn't be complicated or restrictive. As a former certified personal trainer with a bachelor’s degree in Health Behavioral Sciences, Matt brings well-rounded expertise to his blog. From revamping classic recipes with a nutritious twist to breaking down fast food menus, his goal is make healthy living less confusing for everyone. Featured in major publications and with a strong following on social media, Matt is committed to making “healthy” uncomplicated—no matter where you are in your health journey. Join Matt on his mission to simplify health without sacrificing flavor. Learn More

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