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Gluten Free Chocolate Chip Cookie Cups are the perfect easy dessert! These bite-sized cookie cups are crispy outside, chewy inside, and studded with mini chocolate chips. Baked in muffin pans and ready to fill with your favorite toppings!
Classic Chocolate Chip Cookie Cups
I can’t think of many things that are better than a perfect, classic and chewy gluten-free chocolate chip cookie. That is, until I began turning my favorite cookie dough into mini cookie cups, and filled them with chocolate frosting!
Let’s just say, the game is officially changed.
I make these chocolate chip cookie cups in mini muffin tins so that they’re bite-sized. It’s just the best whenever I’m craving a little something indulgent without going completely over the top! Plus, the kids love these. It becomes a whole activity on weekends when we get out toppings like ice cream and sprinkles for filling the individual cups.
Basically, take everything you love about a fresh chocolate chip cookie, and then take it up a notch with these fillable homemade cookie cups!
What You’ll Need
Making chocolate chip cookie cups calls for all the common pantry ingredients that go into a classic cookie. Be sure to scroll down to the recipe card for specific amounts!
- Gluten-Free Flour: For best results, use a 1-to-1 gluten free flour blend such as Bob’s Red Mill, Cup-4-Cup, or King Arthur Flour.
- Leavening: Both baking soda as well as baking powder.
- Butter: Unsalted butter, softened to room temperature (this lets it mix and bake more evenly).
- Sugar: For the perfect chewy texture and slightly caramelized flavor, I use a combination of light brown and granulated sugars when baking chocolate chip cookies.
- Egg: Binds the ingredients and adds richness to the dough.
- Pure Vanilla Extract: Emphasis on pure! Trust me, for the best possible flavor in your homemade cookies, use pure vanilla extract and not imitation.
- Mini Chocolate Chips: The perfect sized chunks of chocolate for these mini cookie cups!
Can I Use Store-Bought Cookie Dough Instead?
You can use any homemade or store-bought gluten-free cookie dough to make these cookie cups. Choose your favorite cookie dough recipe and then just follow the rest of the instructions!
How to Make Gluten-Free Chocolate Chip Cookie Cups
I definitely recommend using silicone muffin pans when making these cookie cups. They can be especially tricky to remove from metal muffin tins.
Make the Cookie Dough: Sift together the flour and dry ingredients in a bowl. In a separate mixing bowl, cream together the butter, sugars, and wet ingredients. Gradually add the flour mixture into the wet ingredients and mix until everything is just combined, then stir in the chocolate chips.
Chill: Place the cookie dough in the fridge to chill for half an hour, or (even better) overnight.
Prep: Once the dough has chilled and while you oven preheats, lightly grease a mini muffin pan and then scoop a spoonful of dough into each well. Gently press the cookie dough into the cups – no need to shape it into the cup completely, as it will bake into shape on its own!
Bake: Bake the cookie cups in a 350ºF oven until the edges are crisp but the middles are still a tad under-baked. Let the cups cool in the pan, then pop them out and get filling! Frost your cookie cups or fill them with ice cream – the possibilities are endless!
Can I Make the Dough In Advance?
Yes! Get a headstart on your cookie cups and mix up the dough per the directions, then portion it out to refrigerate or freeze.
The cookie dough can be kept airtight in the fridge for up to 3 days. Don’t forget to take the dough out of the fridge about a half-hour before baking, to let it come back to room temperature again.
To freeze, portion the dough into balls and store them frozen for up to 3 months. Thaw the dough in the fridge overnight, and let the balls come to room temperature before pressing them into the muffin pan for baking.
Tips for Success
- To Prevent Sticking: Make sure to give your mini muffin pan a light but even coating of non-stick spray to help with sticking. If you’re still concerned that your cookie cups may not pop out so easily, give the wells a light dusting of flour after you’ve sprayed them.
- Don’t Overbake: Your cookie cups are done when they’re still ever so slightly underbaked in the centers. Avoid overbaking, as with most cookies, as this will result in a crunchy, crumbly cookie! The same applies to underbaking, however. If your cookie cups look especially undercooked or wet in the middle, they may need a bit longer in the oven.
See that little dip in the cookie once it’s baked? That spot was destined to be filled with toppings! Use a piping bag to make filling these mini cookie cups even easier. Here are some of my favorite cookie cup toppings:
- Frosting: Pipe your favorite buttercream frosting into these chocolate chip cookie cups. We’re big fans of topping ours with Homemade Chocolate Frosting or Gluten Free Oreo Frosting. For something special and seasonal, try Browned Butter Pumpkin Spice Frosting!
- Peanut Butter: Drop in a spoonful of peanut butter, or frost your cookie cups with a swirl of peanut butter frosting for chocolate and peanut butter cookie cups.
- Cookie Dough: Double the chocolate chip cookie goodness with a dollop of Gluten Free Chocolate Chip Cookie Dough.
- Whipped Cream: A classic and a favorite.
- Ice Cream: These cookie cups are perfect for holding a scoop of vanilla ice cream. You can also get creative with easy homemade ice cream recipes, like this Creamy No-Churn Nutella Toffee Ice Cream.
- Chocolate Mousse: Fill your cups with a classic chocolate mousse or indulge in a grown-ups-only Bailey’s Irish Cream Mousse.
- Cheesecake: Mix up a batch of cheesecake filling and make easy Berry Cheesecake Chocolate Chip Cookie Cups!
- S’mores: Top these cookie cups with chocolate and a fluffy toasted marshmallow for S’Mores Chocolate Chip Cookie Cups.
Toppings don’t end with just the filling! Here are ideas to sprinkle overtop your choice of filling:
- Rainbow sprinkles
- Chocolate shavings
- Hot Fudge Sauce
- Crushed nuts
- Fresh berries
- Maraschino cherries
Keep the baked cookie cups stored airtight on the counter for 3-4 days. I highly recommend storing your chocolate chip cookie cups without fillings until you’re ready to serve them!
Do These Freeze Well?
Like their original chocolate chip cookie counterparts, these cookie cup versions freeze easily for longer storage. Pre-freeze the cups on a baking sheet, or wrap them individually before storing them in a freezer bag or container. They’ll keep fresh when frozen for up to 2 months! Thaw the cookie cups at room temperature before serving.
More Chocolate Chip Cookie Recipes
- Gluten Free Chocolate Chip Cookies
- Flourless Peanut Butter Cookies with Chocolate Chips
- Gluten Free Brookies
- White Chocolate Chip Sugar Cookie Bars
- Chocolate Chip Cookie Pie
Gluten Free Chocolate Chip Cookie Cups
- 2 ¼ cups 1-to-1 gluten-free flour blend (such as Bob's Red Mill, Cup-4-Cup, or King Arthur Flour)
- 1 tsp salt
- 1 tsp baking soda
- 1 tsp baking powder
- 1 cup unsalted butter softened to room temperature
- ¾ cup light brown sugar
- ¾ cup granulated sugar
- 1 large egg
- 2 tsp pure vanilla extract
- ½ cup mini chocolate chips
- In a small bowl, sift together the gluten free flour blend, salt, baking soda, and baking powder. Set aside.
- In a large mixing bowl or the bowl of a stand mixer, add the butter, brown sugar, and granulated sugar. Cream with the paddle attachment at high speed until light and fluffy. Then beat in the eggs and vanilla.
- Turn off the mixer, add the flour mixture, and gradually increase the mixer speed to medium, mixing until just combined. Use a spatula or spoon to stir in the chocolate chips.
- Refrigerate the dough for at least 30 minutes or overnight.
- Preheat the oven to 350°F. Spray a silicone mini muffin pan with nonstick cooking spray.
- Using a cookie scoop or tablespoon, place about 1 Tablespoon of cookie dough into each cup and press it down into the cup.
- Bake the cookie cups for 15-20 minutes or until crisp on the edges but slightly under-baked in the middle.
- Let cool completely in the pan, then pop them out of the pan. Fill with frosting, ice cream, or any other desired fillings.