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Brownie Batter Stuffed Cookie Cups

I’ve been obsessed with my 2 most recent recipes: protein brownie batter, and protein cookie dough.

These recipes are awesome on their own, and I highly recommend checking them out. But, I wanted to take it to the next level. Why not combine the two? Problem is, the cookie dough won’t bake into cookies, as it’s meant to be eaten as a raw dough.

That’s when I remembered that a little while back, I created a keto-friendly chocolate chip cookie recipe. I revisited that recipe as a shot in the dark to see if they’d bake well into cookie cups. Spoiler alert: they worked SO well. It’s rare that a recipe works perfectly on the first try, but that’s exactly what happened here.

This recipe is so incredibly easy and addicting. Each stuffed cookie cup has 250 calories and over 20 grams of protein, which is on-par with any protein bars out there! And I don’t know about you, but I’d choose one of these over a protein bar any day.

Note that this recipe utilizes the brownie batter, but changed it very, very slightly. The original recipe calls for adding melted chocolate, but since these are going to be warmed up in the oven, I decided to omit that part. But if you’ve already made the brownie batter, you can use the original recipe no problem!

Gluten-Free & Keto-Friendly

These are a bit higher in fat than other recipes, but it’s necessary. Trust me, I tried many iterations in my original cookie recipe, and trying to make these lower in fat was a disaster. If you want these to come out tasting like a real cookie, stick with the recipe as-is.

Soft or Crunchy Cookies?

Here’s where you get to have some fun based on your preferences. If you follow the recipe exactly as -is, your cookie cups will be right in the middle: not too soft, and not too crunchy. Since we’re not using any flour or eggs, you can safely undercook these if you want them suuuuper gooey. I would stick to 8 minutes in the oven- any lower, and they may not hold up too well on you.

Prefer crunchy cookies? I put these in the refrigerator and enjoyed them the next day and I think I liked them even more! The cookie crisped up and the brownie batter inside thickened, making these even more enjoyable. If you prefer a crunchy cookie, eat these the following day rather than cooking them longer. This is what it looked like after 24 hours:

So. Good.

No muffin pan?

You can grab a muffin pan off Amazon for very cheap if you need one. With a little nonstick spray, I had no need to use any kind of paper or silicone liners.

If you don’t have a muffin pan, or don’t want to buy one, you can shape these into stuffed cookies on a baking sheet. Follow the instructions below, but when you get to the step with the muffin pan, create cookie shapes with cavities in the middle to hold the brownie batter. I haven’t tried this, but it should work just the same, although they may hold less batter inside.

If you’re curious about certain substitutions, visit the notes below the recipe card.


Brownie Batter Stuffed Cookie Cups

Brownie Batter Stuffed Cookie Cups

Yield: 4 Cookie Cups
Prep Time: 10 minutes
Cook Time: 10 minutes
Total Time: 20 minutes

A combination of two incredible recipes: chocolate chip cookies AND edible brownie batter.


Ingredients for Cookie Cups

  • 42g (1.5 Scoops) Vanilla Whey Protein (I used Bowmar Nutrition)
  • 56g Almond Flour
  • 28g Brown Sugar Substitute (I used Swerve)
  • 1/2 tsp Baking Soda
  • 1/4 tsp Salt
  • 14g Lily's Semi Sweet Chocolate Chips (or mini chocolate chips)
  • 30g Unsweetened Applesauce
  • 21g (1.5 Tbsp) Coconut Oil

Ingredients for Brownie Batter

  • 28g (1 Scoop) Chocolate Whey Protein
  • 35g Canned Pumpkin
  • 20g Brown Sugar Substitute (I used Swerve)
  • 10g Unsweetened Cocoa Powder
  • 8g (1 Tbsp) Peanut Butter Powder (I prefer PBFit)
  • 14g Lily's Semi Sweet Chocolate Chips (or mini chocolate chips)
  • 2 tbsp Sugar-Free Maple Syrup
  • 1/4 tsp Coarse Salt


Directions for Brownie Batter & Cookie Cups

  1. Start with the brownie batter. Combine all of the dry ingredients (protein powder, cocoa powder, powdered peanut butter, and salt) in a bowl and whisk together.
  2. Add in the canned pumpkin, maple syrup, and brown sugar, and use a silicone spatula to mix. It’s going to be thick, so continue stirring until a batter begins to form.
  3. Fold in the chocolate chips, then refrigerate for 1 hour to fully thicken. If you don’t have an hour, you can let it set in the freezer for less time.
  4. Now, move on to creating your cookie dough. Combine all of the dry ingredients for the cookie cups: protein powder, almond flour, brown sugar, baking soda, and salt. Mix together well.
  5. Add the applesauce and coconut oil into your dry mixture. If the coconut oil is not soft enough, throw it in the microwave for 15 seconds or so to help soften it. Keep in mind we don’t want it to be hot- just soft enough to mix in. Use a silicone spatula to fold the mixture and make sure everything is mixed until a dough ball forms.
  6. Fold in the chocolate chips, and then let the dough sit in the refrigerator for one hour as well.

Directions for Stuffed Cookie Cups

  1. After you let both the brownie batter & cookie dough sit for an hour, we’re ready to go! Preheat the oven to 350 degrees F.
  2. Fill a small bowl with cold water to keep near you. The dough is going to be sticky, so lightly dipping your fingers in cold water helps significantly. While working with the dough, be sure to periodically dip your fingers.
  3. Generously spray 4 of the muffin tin cavities with nonstick spray. Take your cookie dough and separate it out into 5 roughly equal sized balls (that’s not a typo, we want 5).
  4. Take 4 of the balls and press them into the muffin tin, shaping them around the edges to create a cup. It’s okay if the cookies feel thin because they will expand when they cook.
  5. Once you have 4 cups, fill each with a spoonful of brownie batter. You should have enough batter to fill each one up pretty well. Here is what mine looked like:
  6. Fold down the edges of the cookie cups to help close them up. This will help create a perimeter, but there will still be a large gap in the center exposing the brownie batter- this is where that extra dough ball comes into play! Seperate that final dough ball into 4 pieces, then flatten them out with your hands (remember to dip them in water) until they’re the perfect size to fit over the top of your cookie cups. Lay them down on top and pinch the edges to ensure they are fully closed. It’s okay if they are not filling the entire space- check out how much mine poofed up!
  7. Add to oven and bake for 10 minutes. If you want slightly softer cookie cups, you should be able to pull them at 8 minutes. Remember that these can be safely undercooked, so you do not need to worry about that! I would not recommend any less than 8 minutes, however, or they might lose their structure.
  8. Let sit for 15 minutes to allow them to cool & finish cooking before removing from the pan. Enjoy immediately, or store these in the fridge to enjoy through the week! The cookies hardened a bit and the brownie batter thickened in the fridge overnight, which ended up making them even better, in my opinion!
Nutrition Information
Yield 4 Serving Size 1 Stuffed Cookie Cup
Amount Per Serving Calories 250Total Fat 13.5gCarbohydrates 13.5gFiber 5gSugar 3.5gProtein 20.5g

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Additional Notes/Substitutions:
  • The pumpkin in the brownie batter helps create the right consistency. If you don’t have pumpkin, or don’t want to use any, unsweetened applesauce might work. But since this recipe is baked, we need an ingredient that will keep the soft consistency, and pumpkin provides that.
  • Remember that the cookies require baking SODA, not baking POWDER. Baking powder will create a poofy cookie and will not taste like the authentic cookie that we’re looking for.
  • You should be able to swap the coconut oil out for butter or another fat. Just keep in mind that the fat is absolutely necessary. I did try these with “light butter” and they did not turn out. At all.
  • You can leave the applesauce out of the cookie cups and add an egg instead, which will give you extra protein and fat. I don’t know exactly how it will work, and it may alter the final properties, but applesauce and eggs are usually pretty interchangeable in recipes.
  • I mentioned it before, but it’s worth repeating- you can safely undercook these if you want them to be softer!
  • If you don’t have brown sugar, you can use regular sugar + maple syrup or honey. I don’t have exact measurements, so it might take some trial & error, but the extra moisture is necessary to prevent these from drying out.
  • I do not count the sugar substitute in my carb count. If you are very strict Keto, you can take those carbs into account and/or change up the quantities. Since sugar substitutes do not count towards the total calories (as they are not utilized by the body) I don’t find it worth counting them towards the totals.

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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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