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Pumpkin Cheesecake Stuffed Protein Cookies

It’s pumpkin season, baby.

Believe it or not, I’m really not a pumpkin spice fan. I absolutely love pumpkin pie, but “pumpkin spice” never really does it for me.

Every single year, my favorite dessert to enjoy at Thanksgiving is pumpkin cheesecake. It’s flavored with actual pumpkin and not just an insane amount of spice, which is exactly what I want.

While I toyed with trying to create a macro-friendly version of that, I decided to go the cookie route instead!

This recipe was inspired by my brownie batter stuffed cookies. If you haven’t tried that recipe, check it out! It’s high-protein brownie batter stuffed inside a chocolate chip cookie, and it’s incredible.

But let’s dive in here…

These cookies are gluten-free AND keto-friendly, so they should appeal to almost everyone!

If stuffed cookies aren’t your thing and you’d rather make regular high-protein pumpkin cookies, check out that recipe here.


Key Ingredients & substitutions

As with all recipes, I know there are going to be substitution questions. Here are the main ingredients used, and what substitutions (if any) you can make:

  • If you’re in a country that doesn’t have canned pumpkin readily available, applesauce works great. If you make that substitution, there won’t be any pumpkin to this recipe, but it will still be a delicious cookie.
  • Remember that these require baking SODA, not baking POWDER. Baking powder will create a poofy cookie and will not be like the authentic cookie that we’re looking for.
  • I’ve made these cookies with regular butter and coconut oil, and both results were great. I tried using light butter to save some calories, but they did not turn out like the cookies I wanted at all. Since these are virtually carb-free, we NEED the fat to produce the end result we’re looking for!
  • These cookies use brown sugar to help them retain moisture. If you do not have brown sugar, regular sugar should still work, but you won’t get quite the same texture.
  • I’ve actually made this recipe with both 100% whey and a blend of whey/casein (PEScience is my go-to) and both worked great. Note that this recipe uses PEScience, which is a blend, and absorbs more liquid than whey alone. If you sue 100% whey, you’ll want to use slightly less pumpkin in this recipe. See the notes in the recipe card for more!


How to Make Pumpkin Cheesecake Cookies

These cookies are not difficult to make, but do require some specific steps to get them just right! So, let’s walk through ’em quickly.

We start by mixing all of our ingredients together to make our cookie dough.

It may seem like there’s not enough liquid, but be patient! Keep mixing and it will turn into a beautiful orange dough.

If you make substitutions, there is a chance you need some extra liquid. If that’s the case, you can add a little extra pumpkin- but keep mixing to let it come together first before making adjustments.

We’re going to chill the dough for one hour- don’t skip this step!! It helps prevent the dough from spreading thin, so we get a nice big cookie when we’re done.

Along with the dough, we’re also going to make a very simple cheesecake filling (like we did with the Protein Strawberry Cheesecake Cupcakes) with cream cheese, some vanilla protein powder, powdered sugar, and vanilla extract. If you don’t want to use protein powder in the filling, you can omit it and just add some extra sugar!

Once everything is mixed and smooth, you just need to spoon it out onto parchment paper or a baking sheet, then freeze for one hour.

Note that I made enough filling for 8 cookies, only to realize I was making 4 cookies instead.

I adjusted the recipe & nutrition accordingly, but that’s why you see more filling than needed!

After an hour, the dough will be very firm and easy to work with.

Form the dough into 8 balls, flatten them out, then add your filling to 4 of your cookies.

Fold the sides up around your frozen filling, then take the other 4 cookies and cover the tops. Pinch the sides and form them into balls.

Sprinkle with a little more cinnamon or pumpkin spice, then pop ’em into the oven. That’s it!


These cookies can be enjoyed immediately, but the filling tastes more on the cream cheese side of things.

If you let these cool in the fridge for an hour (or overnight, which is when this photo was taken), the filling firms up so well and tastes just like a cheesecake filling!

I highly recommend letting them sit to firm up if you can.

If you’re impatient, you can certainly enjoy them right away, but it won’t be quite the same.


Making these as regular cookies

If you want to save some calories and/or don’t feel like making stuffed cookies, you’re in luck!

Soft Pumpkin Protein Cookies

We can make this recipe without the cheesecake filling to not only save calories but also save time!

You can follow the recipe exactly as-is, but form these into 12 small cookies (or however many you’d like) and bake them at 350 degrees F for 8 minutes.

These small cookies will have only 60 calories each (still with 4g of protein) and be ready to enjoy immediately without the need to chill after baking.

I wrote up the full recipe for regular Pumpkin Protein Cookies for you to check out here.


More pumpkin recipes you’ll love

If you’re in the mood for some more pumpkin this Fall, you’re in for a treat…


Pumpkin Cheesecake Cookies

Pumpkin Cheesecake Stuffed Protein Cookies

Yield: 4 Stuffed Cookies
Prep Time: 10 minutes
Cook Time: 10 minutes
Inactive Time: 2 hours
Total Time: 2 hours 20 minutes

A high-protein pumpkin cookie stuffed with a delicious cheesecake filling. Low carb, gluten-free, and 17g protein per cookie.


For Pumpkin Cookies

For Cheesecake Filling


  1. In a large bowl, whisk together the dry ingredients for your cookies (everything except the pumpkin and butter).
  2. Microwave the butter or coconut oil for 30 seconds to soften. We don't need it to be hot, just soft and easy to mix. Add to the bowl with your dry ingredients, along with the pumpkin, and mix until a cookie dough forms.
  3. It will be sticky, but that's okay. Add to the fridge for 1 hour for the dough to thicken up.
  4. Next, make the cheesecake filling by mixing together the cream cheese, protein powder, vanilla extract, and powdered sugar using an electric mixer. If you need to mix by hand and do not have an electric mixer, I recommend leaving the cream cheese out at room temperature to make the mixing process much easier.
  5. Using a spoon, create 4 scoops of the mixture and place them on parchment paper or a baking sheet. Add these to the freezer for 1 hour so they are solidified when we go to bake.
  6. After the dough and filling have chilled for an hour, preheat the oven to 350 degrees F.
  7. Break your dough into 8 roughly equal-sized pieces, then roll them in your palms to create balls and add them to a parchment paper-lined baking sheet. Flatten each one down into a cookie shape.
  8. Take your frozen cheesecake filling and place each in the middle of 4 of your cookies. Using the remaining 4 cookies, cover the cheesecake filling and pinch the edges to create 4 stuffed balls. You can use your hands to make sure everything is completely enclosed.
  9. Bake at 350 degrees F for 10 minutes.
  10. Remove from the oven, sprinkle a little cinnamon on top, and let cool for 10 minutes.
  11. These cookies are best served chilled so the cheesecake filling can solidify inside. Once cooled, add the cookies to a plate and refrigerate for at least one hour (overnight works great) for best flavor.
  12. These cookies will hold up great in the fridge for up to one week!


  • I use PEScience protein, which is a blend of whey & casein protein powder. When I first developed this recipe I used 100% whey protein and can confirm it works well! The only difference is that you'll likely want to use slightly less pumpkin, as whey protein requires less liquid. Start with 40g of pumpkin and only add more if needed.
  • To see how different protein powder affects cookie recipes, check out my Ultimate Protein Powder Substitution Guide.

  • I typically use "light butter" in my recipes to save calories, but these cookies require full-fat butter or coconut oil. Since they are virtually carb-free, the extra fat gets us the texture we want.
  • I do not count sugar substitutes in my carb totals. If you are very strict about carbs, be sure to count those.

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Nutrition Information
Yield 4 Serving Size 1 Cookie
Amount Per Serving Calories 215Total Fat 13gCarbohydrates 7gFiber 2gSugar 4gProtein 17g

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Sunday 2nd of October 2022

Hi, can I omit/substitute protein powders from this recipe?


Monday 3rd of October 2022

I'm not entirely sure, unfortunately. If you're not interested in a high-protein cookie, there are definitely other non-protein options out there if you need a delicious pumpkin cheesecake cookie :]


Sunday 18th of October 2020

Haha thank you Annie! I love big portions, so you can definitely make smaller cookies out of these instead. But, delicious either way!

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