Gluten Free Berry Cookie Cups

Chewy chocolate cookies are topped with a Greek yogurt cheesecake filling and fresh berries in these berry cookie cups. They’re the perfect balance of sweet and tangy and super easy to make. The mini muffin tin makes them the ideal size for sharing at potlucks and picnics, too!

Delicious Details
- Cuisine Inspiration: American
- Primary Cooking Method: Oven
- Dietary Info: Gluten-free option
- Skill Level: Easy
These berry cookie cups have been a huge family favorite since I first made them in 2014. I took them to a family party and immediately had to make a second batch because my son was so upset that he didn’t get to eat one before they were gone. Fast forward over 12 years, and that same level of excitement appears whenever I make them.
What I love about these berry cookie cups is that they turn basic chocolate chip cookie dough into a completely new and elevated experience. When I make these, I start with my gluten free chocolate chip cookie cups, but you can use any cookie dough, even the pre-made kind. Once the dough is baked in a mini muffin tin, the cookie cups are then filled with a tangy no-bake cheesecake filling and topped with fresh berries.
These became the inspiration for other cookie cup flavors, like s’mores cookie cups and pumpkin cookie cups, but these berry cookie cups have remained the most requested. Once you taste them, you’ll understand why!
Why These Berry Cookie Cups Are So Good
- Made for parties. These little berry cookie cups are perfect for a party. They are quick and easy, make a bunch, and perfectly portioned so that you can sample several treats from the dessert table (you know, if you are anything like my kiddo).
- Buttery chocolate chip base. These little treats begin with your favorite chocolate chip cookie dough baked in a mini muffin tin to create a thick cookie cup base. So not only does every bite get you that tangy cheesecake filling and fresh berries, you get a chewy cookie too.
- Easy to make. It takes minimal effort to make these berry cookie cups. And if you want to make it even easier, start with pre-made cookie dough! The only thing to remember is that the cookies need to cool before assembling, so do plan to make them in advance.
- Fresh fruit. Each of these cookie cups is topped with fresh raspberries, strawberries, and blueberries (or any combination you choose). I love the pop of the sweet-tart berries against the tangy filling and sweet cookie base.

Key Ingredients
Below is a list of the ingredients you’ll need to gather to make this cookie cups recipe, plus a few notes to help you out. Scroll all the way down for the full recipe card with measurements.
- Chocolate chip cookie dough – Any chocolate chip cookie dough works here, whether it’s store-bought, from a mix, or homemade.
- Cream cheese – Regular or light cream cheese both work but avoid non-fat cream cheese. It will be too soft, and the filling won’t stay on the cookies.
- Plain Greek yogurt – Takes the place of sour cream in the cheesecake filling while still adding the classic tangy flavor.
- Powdered sugar – Sweetens and stabilizes the cream cheese filling.
- Vanilla extract – Adds flavor to the filling.
- Berries – I used a combination of raspberries, blueberries, and strawberries. Feel free to use any combination of berries that you have on hand.
What Cookie Dough Should I Use?
As I mentioned, you have the option to use your favorite homemade or store-bought, regular or gluten-free cookie dough. Just keep an eye on the baking time, as it may vary from what is suggested in the recipe.
If using store-bought cookie dough, the break-and-bake type is easiest to work with. The brand of gluten free chocolate chip cookie dough I used is no longer on the market, but Immaculate Baking Company has several varieties of pre-made gluten free cookie dough.
The other option is to use your favorite chocolate chip cookie recipe and make the dough from scratch. My gluten free chocolate chip cookie cups are perfect for this recipe, though you can use any recipe and just scoop about a tablespoon into each well of the muffin pan.
🍴 In the Cupcakes & Kale Chips Kitchen…
- Mini Muffin Pan – I like using a silicone muffin pan for making cookie cups because it’s so much easier to pop them out, especially when making gluten free chocolate chip cookie cups, which are a bit more tender than traditional ones.

Recipe Tips & Tricks
- Adjust the baking time as needed. This recipe is based on using my chocolate chip cookie cups dough. Most cookie doughs have a similar baking time, but just keep an eye on the pan if you opt to use a different recipe.
- Only a tablespoon of dough. Remember that you’re not filling the entire muffin well with cookie dough. Just a tablespoon of dough will do, since it’ll rise up a bit in the oven.
- Let the cookies cool. The cookie cups need to be completely cool before adding the cheesecake filling. Otherwise, it’ll just slide right off. Feel free to make them up to a day in advance and keep stored in an airtight container.
- Try a different cookie dough. While I love the addition of the chocolate, these berry cookie cups would also be delicious made with sugar cookie cups.
Proper Storage
- Fridge: Once the cheesecake topping is added, these berry cookie cups must be stored in the fridge. They’re best enjoyed within 1-2 days.
- Freezer: The cookie cups without the topping can be frozen. Flash freeze the cookie cups on a baking sheet, then transfer to an airtight container. Freeze for up to 3 months.

More Cookie Recipes To Try

Berry Cookie Cups
Ingredients
- 1 package chocolate chip cookie dough (regular or gluten free) or homemade cookie dough. You will need about 1 1/2 cups or enough for about 24 cookies (see Note*)
- 16 ounces cream cheese , softened to room temperature (regular or light, NOT fat free)
- ½ cup plain Greek yogurt
- ½ cup powdered sugar
- 2 teaspoons vanilla extract
- 24 raspberries
- 24 blueberries
- 24 strawberry slices
Instructions
- Preheat oven to 350°F and spray a mini muffin tin (with 24 cups) with nonstick cooking spray.
- Divide 1 package chocolate chip cookie dough between the 24 cups, about 1 Tablespoon in each.
- Bake for 12-14 minutes, or according to package directions, until golden brown and crisp.
- Cool in pan for several minutes before removing to cooling rack to cool completely.
- Prepare the cheesecake topping by combining the 16 ounces cream cheese, ½ cup plain Greek yogurt, ½ cup powdered sugar and 2 teaspoons vanilla extract in a large bowl or the bowl of your stand mixer and beat with a hand mixer or stand mixer until smooth.
- Use a small amount of the cheesecake topping to attach one raspberry to the top of each cookie cup.
- Use a piping bag, plastic bag with a hole cut in the cornier to pipe the topping carefully around the raspberry on top of the cookie cup, or spread around it carefully with a knife or spatula. Smooth out the topping with a knife or spatula.
- Garnish each cookie cup with one strawberry slice and one blueberry.




Hi, I have a project where we must use minimal ingredients and find an affordable recipe under $15. Thank you so much for this recipe it helped a lot!
A few questions:
1. Are the cookie ‘cups’ hollow and filled with frosting? Or is it filled with chocolate chip cookies?
2. For the frosting, do you think I could skip the Greek yogurt, or is it essential to the taste of the recipe?
Hi! The cookie cups are not hollow. They are basically chocolate chip cookies baked in the shape of a mini cupcake. You could use another cream cheese frosting recipe, if you prefer. The Greke yogurt adds to the tangy flavor and helps make it creamy. But it is not essential for the taste. However, if you just leave it out, it will likely be too thick. Hope that helps!
Got it! Thanks for the clarification.
What fun and clever idea! They sound and look terrific.
Thanks! They were fun!
These look awesome Brianne 🙂 Love this idea.
I found your recipe over at the Two Cup Tuesday link party. I host Tickle My Tastebuds Tuesday and would love it if you linked up this recipe. I’m sure our party goers would love it as much as I do. Here is the link http://bit.ly/1mF7z6K. Have a wonderful day!!
I have to try the cookie cups! What a nice touch!
Look at how perfectly cute your berry, cheescakey cookie cups are. Love love love!!
Such a perfect dessert for a picnic! Delicious!
What an adorable little treat and such a cute story to go along with it 🙂
You’re lucky that your kids eat pretty much everything you put in front of them. My daughter is really picky. I like the bite size portions of this dessert!