Gluten-Free Cookie Cups

These gluten-free cookie cups are generously packed with chocolate chips and perfectly baked to achieve that golden, chewy edge we all love. Finished with your favorite frosting and a sprinkle of colorful decorations, they're perfect for birthdays, holidays, or any celebration!
Multiple gluten-free cookie cups topped with vanilla frosting and rainbow sprinkles on a wire cooling rack.
Multiple gluten-free cookie cups topped with vanilla frosting and rainbow sprinkles on a wire cooling rack.

Why this recipe works

The gluten-free cookie cups are baked in a muffin tin for a fun, cup-shaped twist on the classic chocolate chip cookie. Filled with a generous amount of your favorite buttercream or frosting and then decorated with rainbow sprinkles, these cookie cups will bring out the kid in everyone!

You’ll love this recipe because:

  • They’re easy to make. Despite their impressive appearance, these cookie cups are surprisingly simple to make. The recipe involves common ingredients and there’s no need to chill the dough before baking it. Just make the dough and place in the cookie cups! 
  • They’re perfect for any occasion. Whether you’re baking for a birthday party, holiday, or just as a treat for yourself, these cookie cups are a hit. The option to decorate them with sprinkles or customize the frosting means they can be tailored to fit any event or celebration.
  • They’re gluten-free. These cookie cups are made gluten-free using an all-purpose gluten-free flour blend like Bob’s Red Mill 1-to-1 Gluten-Free Baking Flour, which contains xanthan gum. I promise you will not be able to tell that these cookie cups are gluten-free! They taste just like their gluten-filled counterparts.

Ingredients

Ingredients in small bowls to make gluten-free cookie cups, including vanilla frosting, rainbow sprinkles, brown sugar, unsalted butter, vanilla extract, baking soda, salt, chocolate chips, gluten-free flour, two eggs, and granulated sugar with text overlays over each ingredient.

Ingredient Notes

  • Gluten-free flour blend – I used Bob’s Red Mill 1-to-1 Gluten-Free Baking Flour (n the blue bag), which is a blend of white rice flour, brown rice flour, sorghum flour, potato starch, and tapioca flour, as well as xanthan gum. I cannot verify that other gluten-free flour blends will deliver the same success in this recipe since I haven’t tried them yet. 
  • Baking soda – Ensure that your baking soda is fresh for best results. 
  • Salt – I used table salt, but you can also use kosher salt for this recipe. 
  • Unsalted butter – Use unsalted butter so that you can control the salt level in the cookie dough. Ensure butter is at room temperature so it creams well with the sugars. 
  • Granulated sugar and brown sugar – I like to use a combination of granulated sugar and brown sugar in my cookie recipes. I use light brown sugar for its mild molasses flavor, but dark brown sugar can be substituted for a deeper, more caramel-like taste. 
  • Eggs – Use large eggs, 50g each, for this recipe. Ensure they are at room temperature so they incorporate into the cookie dough easily. 
  • Vanilla extract – Use pure vanilla extract for best flavor. 
  • Chocolate chips – Semi-sweet chips are a classic choice, but feel free to use dark, milk, or even white chocolate chips depending on your preference.
  • Frosting or buttercream – Choose any flavor you like or make your own. If you’re short on time, store-bought can work just as well. Some of my favorite frostings to use for this recipe are brown butter cream cheese frosting, chocolate cream cheese frosting, and peanut butter frosting
  • Rainbow sprinkles – Sprinkles add a fun, festive touch but can be omitted if desired. Be sure that your sprinkles are gluten-free, as not all brands are. 

Measuring gluten-free flour the right way is super important to make sure your cookies turn out just right. I love using a kitchen scale to weigh the flour—it’s super easy and you can’t beat the accuracy. Since gluten-free ingredients can be a bit pricey, spending around $10 on a food scale is a worthwhile investment for ensuring consistent, precise outcomes. If you don’t have a scale, use the spoon and level method for measuring flour instead. Gently spoon the flour into your measuring cup and level it off with the back of a knife. This trick keeps the flour light and fluffy, so your cookies won’t end up too heavy.

Step-by-Step instructions

These gluten-free cookie cups with vanilla frosting are super simple to make with just a few ingredients you probably already have on hand! You can use your favorite homemade frosting or a can of store-bought frosting. Either works! The below photos with matching steps are not meant to be the full recipe, but are there to help you see the recipe made at various stages so you can make these chocolate chip cookie cups perfectly every time.

For the ingredient list with measurements, full instructions, printable recipe, and additional notes, please scroll down to the recipe card.

A glass mixing bowl with gluten-free flour, salt and baking soda before being whisked together.
Add the gluten-free flour, baking soda and salt to a mixing bowl. Whisk to combine. Set aside.
A glass mixing bowl with butter, brown sugar and granulated sugar that has been creamed together.
In a separate mixing bowl, add the butter, brown sugar, and granulated sugar. Cream together.
A glass mixing bowl with a creamed butter and brown sugar mixture that has been mixed together with eggs and vanilla extract.
Add the eggs and vanilla extract. Mix until smooth.
A glass mixing bowl with a gluten-free cookie dough that has been mixed together.
Gradually add the dry ingredients to the wet ingredients. Mix until no more streaks of flour remain.
A glass mixing bowl with gluten-free cookie dough topped with a pile of semi-sweet chocolate chips before mixing together.
Add the chocolate chips to the cookie dough. Mix to combine.
A portion scoop filled with gluten-free chocolate chip cookie dough over a glass mixing bowl of additional cookie dough.
Use a portion scoop to measure out the dough into 2-3 tablespoon sized balls.
A muffin tin that has scoops of gluten-free chocolate chip cookie dough in the center of each muffin well before baking in the oven.
Place the cookie dough balls in a greased muffin tin. You should be able to fill 18 muffin wells. Bake the cookies until golden on the wedges and no longer raw in the center.
A tablespoon-sized measuring spoon pressing down in a chocolate chip cookie cup in a muffin tin to make an indentation after baking in the oven.
While still warm, use a measuring spoon to lightly press an indentation into the center of each cookie cup.
An overhead view of muffin-shaped cookie cups in a muffin tin that have been pressed down in the center of each cookie cup to make an indentation for frosting.
Let the cookie cups cool completely before decorating.
Three gluten-free cookie cups topped with vanilla frosting and rainbow sprinkles on a pink dessert plate with additional cookie cups in the background.
Pipe your favorite buttercream or frosting into the center of each cookie cup and decorate with sprinkles. Serve and enjoy!

Recipe FAQs

Which gluten-free flour blend is best for this recipe?

I tested this recipe with Bob’s Red Mill 1-to-1 Gluten-Free Baking Flour in the blue bag. You can buy this flour blend at many local grocery stores and national big box stores, like Walmart and Target. I cannot verify that other brands of gluten-free flour will work in this recipe, as I have not tested them. Not all gluten-free flours behave the same way because they are made up of different ingredients to try to mimic the flavor and texture of all-purpose flour.

How do I prevent the cookie cups from sticking to the muffin tin?

Ensure you generously grease the muffin tin with non-stick cooking spray or use muffin liners. If they still stick, running a knife or a thin spatula around the edges of the cups after cooling can help release them without breaking. You can also use parchment liners if you prefer like I do in my peanut butter cup cookies recipe

How do I know when the cookie cups are done baking?

The edges should be golden brown, and the centers should be set but not too hard. If you gently press the middle and it feels slightly soft but not raw, they’re done. Remember, they will continue to firm up as they cool in the tin.

Can I make these in mini muffin tins instead of regular sized muffin tins?

Yes, you can. You will get about triple the yield using mini muffin tins. The mini cookie cups will bake much faster than regular sized ones, so check the oven at about 9-10 minutes instead. 

expert tips

  • For cookie cups that bake evenly and look uniform, use a cookie scoop or measuring spoon to portion your dough. This ensures that all your cups are the same size and cook at the same rate. I used a yellow portion scoop (#20 scoop) which is about 3 tablespoons. 
  • After baking, use a rounded utensil like the back of a tablespoon or a small jar to press the center of each cookie cup. Doing this while they’re still warm helps create a perfect cavity for the filling but be gentle to avoid cracking. You can also skip this step if you prefer, but you will not be able to fill the cookie cups with as much frosting.
  • Avoid overbaking. Cookie cups continue to bake and set in the hot pan even after you remove them from the oven. Pull them out when the edges are set but the centers are slightly underdone to avoid dry, hard cups.
  • Customize your fillings. Beyond traditional frostings or buttercreams, consider filling your cookie cups with lemon curd, chocolate ganache, or even a no-bake cheesecake filling. The options are endless and can be adjusted according to the occasion or season.

Storage instructions

  • Storage: Keep cookie cups in an airtight container at room temperature for up to 3 days for optimal freshness. If they are frosted or filled with a perishable ingredient (like cream-based frostings), store them in the refrigerator in a tightly sealed container for up to 5 days.
  • Freezer Option: Cookie cups can be frozen for longer storage. To freeze, place the completely cooled cookie cups (frosted or unfrosted) on a baking sheet and freeze them until solid. Once frozen, transfer them to a freezer-safe bag or container, separating layers with parchment paper to prevent sticking. They can be stored in the freezer for up to 2 months. 
  • Reheat/Thaw:

A chocolate chip cookie cup filled with vanilla frosting and topped with rainbow sprinkles that has a bite taken out of it.

Did you make this recipe?

I’d love to know! Please rate it and leave a comment below. You can also share your pictures and tag @adashofmegnut on Instagram.

Multiple gluten-free cookie cups topped with vanilla frosting and rainbow sprinkles on a wire cooling rack.

Gluten-Free Cookie Cups

These gluten-free cookie cups are generously packed with chocolate chips and perfectly baked to achieve that golden, chewy edge we all love. Finished with your favorite frosting and a sprinkle of colorful decorations, they're perfect for birthdays, holidays, or any celebration!
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Course: Dessert
Cuisine: American
Diet: Gluten Free
Prep Time: 10 minutes
Cook Time: 16 minutes
Cooling Time: 30 minutes
Total Time: 56 minutes
Servings: 18 cookie cups
Calories: 390kcal
Author: Megan

Ingredients

  • 2 1/2 cups gluten-free flour blend (350g, I used Bob's Red Mill 1-to-1 Gluten-Free Baking Flour (in the blue bag))
  • 1 teaspoon baking soda (7g)
  • 1 teaspoon salt (7g)
  • 3/4 cup unsalted butter (at room temperature (170g))
  • 1 cup brown sugar (200g)
  • 1/2 cup granulated sugar (100g)
  • 2 large eggs (100g)
  • 1 tablespoon vanilla extract
  • 1 1/2 cups chocolate chips (263g)
  • 2 cups frosting or buttercream (of choice)
  • 1/4 cup gluten-free rainbow sprinkles (optional)

Instructions

  • Preheat the oven to 350°F (175°C). Grease 18 cups of a regular sized muffin tin with nonstick cooking spray or use muffin liners to prevent sticking. Set aside.
  • In a medium mixing bowl, combine the gluten-free flour blend, baking soda, and salt. Set aside.
  • In a separate large mixing bowl, add the room temperature butter, brown sugar and granulated sugar.
  • Cream with an electric mixer for 2-3 minutes, until light and fluffy, scraping down the sides of the bowl with a spatula as needed.
  • Add the eggs and vanilla extract to the creamed butter mixture. Mix until smooth.
  • Add half of the dry ingredients to the butter mixture and stir until just combined. Repeat with the remaining flour mixture, stirring until no more streaks of flour remain.
  • Stir in the chocolate chips until distributed throughout the cookie dough.
  • Scoop the dough into 2-3 tablespoon balls and place in each greased muffin well. You should be able to fill about 18 muffin cups.
  • Bake at 350°F (175°C) for 14-16 minutes, until the edges are golden brown and the center is set. Remove from the oven and let cool for a few minutes.
  • Then, use a tablespoon or other rounded object to indent the cookie cups in the center while the cookies are still warm. This will give you plenty of room for the frosting.
  • Allow the cookie cups to cool in the muffin tin for about 10 minutes before transferring them to a wire rack. This helps them set properly and makes removal easier without breaking. Let the cookie cups cool completely before decorating.
  • Frost with your favorite buttercream once cool and decorate with sprinkles.
  • Serve and enjoy!

Notes

  • This recipe was tested with Bob’s Red Mill 1-to-1 Gluten-Free Baking Flour (in the blue bag), which already contains xanthan gum. I cannot verify that other brands of gluten-free flour will work in this recipe, because I have not tested them. 
  • For best results, weigh your gluten-free flour blend with a kitchen scale to ensure accuracy. If using cups, spoon the flour into the measuring cup and level it off with a knife to avoid packing.
  • You can use your favorite homemade frosting or buttercream in this recipe or you can use store-bought canned frosting to simplify the recipe. Either will work!
  • Ensure that your sprinkles are gluten-free as some have gluten added to the ingredients list. 

Nutrition

Calories: 390kcal | Carbohydrates: 59g | Protein: 3g | Fat: 16g | Saturated Fat: 8g | Polyunsaturated Fat: 2g | Monounsaturated Fat: 3g | Trans Fat: 0.3g | Cholesterol: 41mg | Sodium: 258mg | Potassium: 35mg | Fiber: 2g | Sugar: 45g | Vitamin A: 296IU | Vitamin C: 0.1mg | Calcium: 45mg | Iron: 1mg
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about megan

I’m Megan

A gluten-free food blogger from Chicago and lover of all things food, showing you gluten-free can be easy and delicious, too. Let’s make gluten-free stress free together! Read more…

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