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Healthy Pumpkin Cheesecake Cookies (High Protein & Low Carb)

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, definitely check it out. It’s high-protein brownie batter stuffed inside a chocolate chip cookie, and it’s incredible.

But these stuffed pumpkin cheesecake cookies may just have them beat.

Pumpkin Cheesecake Protein Cookies

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

Each stuffed cookie contains 145 calories, 9g fat, only 4.5g carbs, and a whopping 12g of protein.

And if you want to turn these into lower-calorie cookies by leaving the cheesecake filling out, you can turn to my Protein Pumpkin Cookies, which have only 60 calories per cookie!


Key Ingredients for these pumpkin cheesecake cookies

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

  • 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 cakey 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! Butter adds some extra calories, but it is completely worth it.
  • These cookies use brown sugar to help them retain moisture. If you do not have brown sugar, regular sugar should still work, especially because it’s not a very large amount of sugar we are using.
  • I’ve actually made this recipe with both 100% whey and a blend of whey/casein (PEScience is my go-to brand) and both worked great. Note that this recipe uses PEScience, which is a blend, and absorbs more liquid than whey alone. If you use 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 healthy pumpkin cheesecake cookies

Even though these cookies are stuffed, you do not need to be intimidated. These pumpkin cheesecake cookies are surprisingly simple to throw together.

First, we’re going to mix up all of our ingredients to make the pumpkin cookie dough except for the protein powder. When we do this, it’s going to leave us with a paste-like mixture.

Something I’ve learned in my years of baking with protein powder is that adding the protein powder as your final ingredient helps reduce the overall stickiness. If you add the protein powder with the rest of the ingredients, oftentimes it will lead to a very sticky dough.

By adding it last, the protein powder acts as a thickener and absorbs a lot of the liquid, leading to workable cookie dough.

highly recommend using PEScience, which is a blend of whey & casein protein powder, to achieve the best consistency. 100% whey protein works for this recipe, but I haven’t tested any other types of protein powder for this one.

At the time of writing this, PEScience has pumpkin pie protein available, which I cannot recommend enough. It may just be my favorite flavor. If it is not available, vanilla works great. We’re adding some spice to the batter, so vanilla works just fine (and don’t forget to use my code “Matt” at checkout to save money if you do pick up some protein).

We’re going to chill the pumpkin cookie dough for one hour- don’t skip this step!

Chilling the dough will not only make it easier to work with, but it will also lead to an authentic cookie texture once baked. If you want a true cookie, chilling this dough is pivotal.

Likewise, we’re going to mix up a very simple cheesecake filling made up of fat free cream cheese, protein powder, vanilla extract, and powdered sugar, and refrigerate that as well. Note that I used fat-free cream cheese to keep the calories lower, but you can use any cream cheese for this recipe.

It’s going to be a pretty loose mixture, but it thickens up in the fridge and you’ll be able to grab small spoonfuls of it.

As you can see from my photo, the cheesecake filling does not need to be perfectly smooth, you just want to make sure that there isn’t any dry powder left.

After the dough and cheesecake filling have chilled, it’s time to form some pumpkin cheesecake cookies.

We’re going to take a small cookie scoop to scoop 12 small pieces of the pumpkin cookie dough, then we’re going to flatten those into discs.

The cheesecake filling is going to be scooped out and added to the center of half of the cookies. When you do this, make sure there is room around the outside so you can easily seal them.

Cover the cheesecake filling with the other pieces of cookie dough, then pinch down the edges. Pick each stuffed cookie up and form it into a ball in your hands, sealing any cracks that may have formed.

As long as the cheesecake filling is completely enclosed in the pumpkin cookie dough, you’re ready to go.

Place back on the baking sheet and bake at 350 degrees F for 10 minutes.

After 10 minutes, the cookies will come out looking a little bit puffed up, but they will set as they cool.

I like to let these cookies cool for 10 minutes, then place them in the fridge to fully set for about 1 hour. I know that waiting an extra hour is tough, but it’s necessary for the cheesecake filling to firm up inside of the cookies.

These cookies can be enjoyed immediately, but the cheesecake filling is going to be a warm, runny cream cheese, which is definitely not what we are after.

The flavors of these pumpkin cheesecake cookies really develop as they sit as well, so you’ll find they may even taste better the following day.

Keep any leftover cookies in the fridge and enjoy them throughout the week! These pumpkin cheesecake cookies will remain incredibly soft even as leftovers.


Baking these are regular pumpkin cookies

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

Pumpkin cookies on table

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

The only downside to baking with canned pumpkin is that once you open a can, you have to use it up relatively quickly before it goes bad on you.

To help you out, here are some other recipes of mine that will help you get through that canned pumpkin.


Healthy Pumpkin Cheesecake Cookies (High Protein & Low Carb)

Healthy Pumpkin Cheesecake Cookies (High Protein & Low Carb)

Yield: 6 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 12g protein per cookie.


For Pumpkin Cookies

For Cheesecake Filling


  1. Microwave the butter or coconut oil for 30 seconds to melt. Mix together with the canned pumpkin in a large bowl.
  2. Add the rest of the cookie ingredients except for the protein powder, then mix it up until there is no powder left.
  3. Mix the protein powder last to act as a thickener and bring everything together to form cookie dough.
  4. Rrefrigerate the cookie dough for one hour. You can skip this if you are really pressed for time, but chilling the dough is going to lead to a much better cookie consistency once baked.
  5. Make the cheesecake filling by mixing together your cream cheese, protein powder, powdered sugar, and vanilla extract in a small bowl until smooth. Add this to the fridge for one hour to chill & thicken while the cookie dough chills.
  6. After the dough and filling have chilled for one hour, preheat the oven to 350 degrees F.
  7. Use a small cookie scoop to scoop 12 small cookies out of your dough and place on a parchment paper-lined baking sheet. If you do not have a cookie scoop, you can use a small kitchen spoon.
  8. Using your fingers, press the cookie dough balls down into discs. Take a small amount of your cheesecake filling and place it in the center of 6 of the cookies. The amount you use is totally up to you, just be sure to leave some room around the edge of the cookie to seal it up. Note: I had a little bit of leftover filling, but not much.
  9. Take the other 6 pieces of cookie dough and place them over the top of the cheesecake filling, then pinch down the edges. Pick up the stuffed cookies and form them into balls, patching up any cracks to make sure the cheesecake filling remains inside of the cookies.
  10. Bake at 350 degrees F for 10 minutes.
  11. Rremove the pumpkin cheesecake cookies from the oven, and let them cool for one hour. You can eat them before the one hour mark, but the cheesecake filling inside will be soft. I like to let these cool for 5-10 minutes, then place them in the fridge for one hour to allow the cheesecake filling to fully set.
  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.
  • 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 authentic cookie consistency we want.
  • I used fat-free cream cheese and it worked really well in this recipe. if you use a different type of cream cheese, just note that the calories are going to be a bit higher.
  • 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 6 Serving Size 1 Cookie
Amount Per Serving Calories 145Total Fat 9gCarbohydrates 4.5gProtein 12g

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Saturday 3rd of February 2024

Allergic to almonds. Substitute?

Matt Rosenman

Wednesday 14th of February 2024

I love using oat flour in cookies. It won't be a perfect sub for almond flour because almond flour contributes a good amount of fat & moisture, but oat flour tends to work well for cookies in my experience.


Wednesday 19th of October 2022

I can't wait to make these! Where do you live that you can still get fat free cream cheese?!?! It has disappeared from VT.


Friday 28th of October 2022

@Katy, It disappeared where I live (Michigan) for the longest time, too! It just recently came back so I took full advantage. Maybe it's making a comeback?


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!

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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