Gluten-Free Cookie Cups

These gluten-free cookie cups are a fun twist on classic chocolate chip cookies. Instead of baking flat on a sheet pan, the dough goes into a muffin tin so each cookie bakes into a cup shape with chewy edges and a soft center. Once they cool, you fill them with frosting and top with sprinkles.

The base is a straightforward chocolate chip cookie dough made with Bob’s Red Mill 1-to-1 gluten-free flour. No chill time, no complicated steps, and the whole batch is done in under an hour.

Why You’ll Love this Recipe

• Easy to make. No chill time and no special equipment. Just mix, scoop into a muffin tin, and bake.
• Perfect for any occasion. Customize the frosting and sprinkles to match birthdays, holidays, or any celebration.
• Endlessly fillable. Go beyond frosting with chocolate ganache, lemon curd, or no-bake cheesecake filling.
• Gluten-free and no one will know. These taste just like classic chocolate chip cookie cups you’d find at the cookie stand at the mall.

Ingredient Notes

• Gluten-Free Flour Blend – I used Bob’s Red Mill 1-to-1 Gluten-Free Baking Flour (in the blue bag), which contains xanthan gum. I cannot verify that other gluten-free flour blends will deliver the same results in this recipe.
• Unsalted Butter – Use room temperature butter so it creams smoothly 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) at room temperature so they incorporate easily.
• Chocolate Chips – Semi-sweet is classic, but dark, milk, or white chocolate chips all work.
• Frosting or Buttercream – Homemade or store-bought both work. Some of my favorites 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 are optional. Be sure that your sprinkles are gluten-free, as not all brands are.

Why I Include Metric Measurements

Weighing your gluten-free flour with a kitchen scale is the single best thing you can do for consistent results in this recipe. If you don’t have one, use the spoon and level method. Gently spoon flour into the measuring cup and level it off with a knife. Scooping directly from the bag packs in too much flour and makes the cookies dense.

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! 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.

Add the gluten-free flour, baking soda and salt to a mixing bowl. Whisk to combine. Set aside. In a separate mixing bowl, add the butter, brown sugar, and granulated sugar. Cream together. Add the eggs and vanilla extract. Mix until smooth. Gradually add the dry ingredients to the wet ingredients. Mix until no more streaks of flour remain. Add the chocolate chips to the cookie dough. Mix to combine. Use a portion scoop to measure out the dough into 2-3 tablespoon sized balls. 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. While still warm, use a measuring spoon to lightly press an indentation into the center of each cookie cup. Let the cookie cups cool completely before decorating. 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). I cannot verify that other brands will work, as not all gluten-free flour blends behave the same way.

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

Generously grease the muffin tin with nonstick cooking spray or use parchment liners. If they still stick, run a thin spatula around the edges after cooling to release them without breaking. You can also use parchment liners if you prefer like I do in my gluten-free 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 hard. If you gently press the middle and it feels slightly soft but not raw, they’re done. 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

• Portion evenly. Use a cookie scoop or measuring spoon so the cups bake at the same rate. I used a #20 scoop, which is about 3 tablespoons.
• Press while warm. Use the back of a tablespoon or a small jar to press the center of each cup right after baking. This creates a deep cavity for frosting. Be gentle to avoid cracking.
• Don’t overbake. Cookie cups continue to set in the hot pan after you pull them from the oven. Take them out when the edges are golden but the centers still look slightly underdone.

Storage Instructions

• Room temperature: Store unfrosted cookie cups in an airtight container for up to 3 days. If frosted with a cream-based frosting, store in the refrigerator for up to 5 days.
• Freezer: Place cooled cookie cups on a baking sheet and freeze until solid, then transfer to a freezer-safe bag or container with parchment between layers. Store for up to 2 months.
• Reheating: Thaw frozen cookie cups at room temperature for about 30 minutes. For a warm, fresh-baked texture, reheat unfrosted cups in a 300°F oven for 3-5 minutes. Add frosting after reheating.