Pumpkin Chocolate Chip Cookie Cups

These pumpkin chocolate chip cookie cups are baked in a mini muffin tin and filled with pumpkin cream cheese frosting. With warm spices, little chocolate chips and a creamy center, they’re a fun fall dessert to share with family and friends.

Hi friends! Danae here from Recipe Runner. It took me a little while to admit summer was coming to an end, but now I’m ready for fall baking and all things pumpkin. These little cookie cups seemed like a fun way to get started!

I love making cookie cups because the mini muffin pan keeps them from spreading, and pressing down the warm centers makes a little spot for pumpkin cream cheese frosting. Plus, I can never resist a miniature dessert. With mini chocolate chips tucked into the dough, these little cups have everything I want in a fall treat!

Is This the Right Recipe for You?

• You love pumpkin and chocolate together. These cups have spiced pumpkin cookie dough, mini chocolate chips and pumpkin cream cheese frosting.
• You prefer soft cookies with a creamy finish. The tender cookie base and smooth frosting make these a good choice when you want something beyond a plain chocolate chip cookie.
• You want a small dessert to share. The mini size works well for fall gatherings or a dessert tray where everyone can try a few treats.
• You enjoy baking from scratch. You’ll make both the cookie dough and frosting with a mixer and bake the cups in a mini muffin pan.
• You have time for cooling and filling. Each batch bakes in 7 to 9 minutes, but the cups need to cool completely before you add the frosting.

Ingredients You’ll Need

You’ll find the full ingredient list and measurements in the recipe card below. Here are a few things to know before you start.

• Whole wheat pastry flour: This gives the cookies a whole grain base with a finer, more tender texture than regular whole wheat flour. Check the package for the word “pastry.”
• Pumpkin puree: Use plain pumpkin puree, not pumpkin pie filling, which already contains sweetener and spices. You’ll need some for the cookies and a little more for the frosting.
• Cinnamon, ginger and cloves: These give the cookie dough its warm fall flavor.
• Unsalted butter: Let it soften so it blends easily with the pumpkin and sugars.
• Brown sugar and granulated sugar: The combination adds sweetness, with a little molasses flavor from the brown sugar.
• Mini chocolate chips: Their small size works especially well in these little cups and makes the chocolate easier to distribute throughout the dough.
• Low-fat cream cheese: Use softened block cream cheese for the frosting. Spreadable cream cheese from a tub can give you a softer filling.
• Powdered sugar: Sweetens the frosting while keeping it smooth. Break up any noticeable lumps before mixing.
• You’ll also need an egg, vanilla extract, baking soda and salt.

How to Make Pumpkin Chocolate Chip Cookie Cups

Bake the cookies in a mini muffin tin, gently press a well into each warm center, then fill the cooled cups with pumpkin cream cheese frosting.

1. Prepare the oven and pan

Preheat the oven to 375°F. Spray a 24-cup mini muffin tin with cooking spray, coating the bottom and sides of each well so the cookies release easily.

2. Beat the wet ingredients

Using a stand mixer fitted with the paddle attachment or a handheld mixer, beat the softened butter, pumpkin puree, brown sugar and granulated sugar on medium-high speed for about 3 minutes.

Scrape down the sides and bottom of the bowl with a rubber spatula. Add the egg and vanilla, then beat for 1 more minute, until incorporated.

3. Mix in the dry ingredients

In a separate bowl, whisk together the flour, cinnamon, salt, ginger, baking soda and cloves. Add the dry ingredients to the wet mixture and beat on medium-low speed just until you no longer see dry flour.

Fold in the mini chocolate chips with a rubber spatula, scraping along the bottom of the bowl to distribute them throughout the dough.

Pro tip: Start the mixer on low when adding the flour to keep it from puffing out of the bowl. Stop mixing once the dough comes together to help keep the cookies tender.

4. Scoop and bake

Use a small 2-teaspoon cookie scoop to portion the dough into the prepared mini muffin tin. Keep the portions about the same size so they bake evenly.

Bake for 7 to 9 minutes, checking at 7 minutes. The edges should look set and the tops should no longer appear wet, though the cookies will still be soft. Don’t wait for them to become firm and crisp.

5. Shape the cups and let them cool

Immediately after removing the pan from the oven, gently press the back of a small spoon or measuring spoon into the center of each cookie. Make a shallow well for the frosting without pressing through the bottom.

Once the cookies are sturdy enough to lift without bending or breaking, carefully transfer them to a wire rack to cool completely. If needed, let the pan cool and spray it again before baking any remaining dough.

Pro tip: If the spoon sticks, lightly coat its back with cooking spray.

6. Make the pumpkin cream cheese frosting

Using a stand mixer fitted with the whisk attachment or a handheld mixer, beat the softened cream cheese, powdered sugar, pumpkin puree, vanilla and pinch of salt until smooth and fluffy. Scrape down the bowl as needed so no lumps of cream cheese remain.

Cover and refrigerate the frosting for about 30 minutes to help it firm up for piping. This chilling step is optional if you prefer to spoon the frosting into the cups.

7. Fill and finish

Pipe or spoon the frosting into the center of each completely cooled cookie cup. Top with extra mini chocolate chips, if desired, and refrigerate until serving.

Pro tip: Check the bottoms of the cookie cups before filling them. If they still feel warm, give them more time to cool so the frosting doesn’t soften and lose its shape.

Storage and Freezing

Refrigerator: Store the filled cookie cups in an airtight container in the refrigerator and enjoy within 3 days. Keep them in a single layer so the frosting doesn’t get flattened.

Make ahead: You can bake the cups and prepare the frosting a day ahead. Cool the cookies completely, then store the cookies and frosting in separate airtight containers in the refrigerator. Fill them before serving.

Freezer: For the best frosting texture, freeze the cookie cups without the filling. Place the cooled cups in a freezer-safe container with parchment between layers and freeze for up to 2 months. Thaw while covered, then add freshly made frosting.

These are ready to eat chilled, so there’s no need to reheat them.

Frequently Asked Questions

Can I just add pumpkin puree to a cookie mix?

Adding pumpkin puree to a cookie mix changes the dough’s moisture balance, so it isn’t a direct shortcut for these cookie cups. Use a recipe developed for that mix and added pumpkin, or follow the homemade dough below for this version.

Why is my pumpkin cream cheese frosting too soft?

Warm ingredients, watery pumpkin puree or spreadable cream cheese can make pumpkin cream cheese frosting too soft. Use block cream cheese and the measured amount of pumpkin, then refrigerate the frosting for about 30 minutes before filling the cookies. If it’s still too soft to hold a piped swirl, spoon it into the wells instead.

Can I make pumpkin cookie cups in a regular muffin pan?

A regular muffin pan would require different dough portions and a longer baking time, so it isn’t a direct swap for this recipe. These cookie cups were developed for a mini muffin tin, and the larger size hasn’t been tested.

Do pumpkin cookie cups with cream cheese frosting need to be refrigerated?

Yes, these pumpkin cookie cups need to be refrigerated once they’re filled with cream cheese frosting. Store them in an airtight container in a single layer to protect the frosting and help keep the cookies from drying out.

More Recipes Like This

Keep the fall baking going with another pumpkin treat.

• Soft Pumpkin Chocolate Chip Cookies: The same pumpkin-and-chocolate pairing in a classic cookie.
• No Bake Mini Pumpkin Cheesecakes: Another individually portioned pumpkin dessert, with a creamy cheesecake filling.
• Chocolate Pumpkin Fudge: Layers of chocolate and pumpkin with a pecan topping.
• Baked Pumpkin Donuts: A pumpkin treat finished with cinnamon sugar.

Made these Pumpkin Chocolate Chip Cookie Cups? Leave a review and let me know how they turned out!