Chocolate Chip Cookie Dough Cupcakes Recipe with Gooey Centers

These Small Batch Chocolate Chip Cookie Dough Cupcakes are tender vanilla cupcakes filled with edible chocolate chip cookie dough and finished with a creamy chocolate chip cookie dough buttercream. They’re rich, playful, and perfect when you want a small batch treat—this recipe yields six cupcakes.

Small batch chocolate chip cookie dough cupcakes on a white marbled background.

Why you’ll love this recipe

I’m thrilled to add these small batch chocolate chip cookie dough cupcakes to my collection. Each component can be prepared ahead of time and assembled later, which makes them ideal for busy days or when you want to bake just a few treats. I used Wilton wave liners; the recipe makes six cupcakes.

The vanilla cupcakes are based on a small-batch vanilla cupcake method, while the edible cookie dough and cookie dough buttercream are adapted from my cookie-dough-focused recipes. The buttercream has just the right balance of brown sugar and vanilla and is studded with mini chocolate chips for texture.

If you enjoy small-batch baking, try other recipes from the same collection for more single- or six-serving desserts.

Chocolate chip cookie dough cupcake cut in half on a brown cupcake liner.

Ingredients
Substitutions
How to Heat Treat All-Purpose Flour
How to Make the Recipe
Helpful Tips
Recipe FAQs
More Small Batch Cupcakes Recipes!
Chocolate Chip Cookie Dough Cupcakes Recipe

Ingredients

The photos show the ingredients used for this small batch chocolate chip cookie dough cupcake recipe. Below are a few important notes about specific items you’ll need.

Heat-treated all-purpose flour. Use flour that has been heat-treated for the edible cookie dough and for the buttercream. If you can’t purchase heat-treated flour, see the instructions below for a simple oven method. Do not use refrigerated commercial cookie dough for the edible cookie dough filling.
Whole milk. The recipe calls for whole milk for both texture and flavor, but you can substitute lower-fat milk if preferred.
Mini semi-sweet chocolate chips. Mini chips are recommended so the cookie dough pieces remain bite-sized and the frosting pipes smoothly. Regular-size chips are too large for this application.

For exact measurements and full instructions, see the recipe card below in the recipe section.

Substitutions

This recipe uses standard ingredients and does not include dairy-free or egg-free substitutions for the cupcakes. The edible cookie dough is egg-free. If you need alternative ingredients, plan on adjusting texture and baking times; I did not test substitutes for this version.

How to Heat Treat All-Purpose Flour

Raw flour can contain harmful bacteria, so heat-treat any flour used in the edible cookie dough or cookie-dough buttercream. Heat-treating is simple and keeps the dough safe to eat.

To heat treat flour:

Preheat the oven to 300°F (150°C).
Spread the needed flour in an even layer on a rimmed baking sheet.
Bake for 10 minutes, stirring every 2–3 minutes, until the flour reaches 160°F (71°C) with a digital thermometer.
Let the flour cool completely (about 25–30 minutes), breaking up any clumps with a fork. Store in an airtight container until ready to use.

How to Make the Recipe

Below is an overview of how to make these chocolate chip cookie dough cupcakes. The recipe card that follows includes exact quantities and step-by-step instructions.

Edible Chocolate Chip Cookie Dough

Recipe tip: Make the edible cookie dough first so it has time to chill while you prepare the cupcakes and frosting. Use only heat-treated flour for this component.

Granulated sugar, light brown sugar, butter, and vanilla extract added to a small glass mixing bowl on a white marbled background.

Step 1. Cream together butter, granulated sugar, and light brown sugar with vanilla until light and fluffy.

Added heat treat all purpose flour, salt and whole milk to edible cookie dough batter in a glass mixing bowl.

Step 2. Mix in heat-treated flour, a pinch of salt, and whole milk until combined. If it’s slightly dry, add a teaspoon of milk.

Folding mini chocolate chips into edible chocolate chip cookie dough mixture in a glass mixing bowl on a white marbled background.

Step 3. Fold in the mini semi-sweet chocolate chips.

Glass mixing bowl with edible chocolate chip cookie dough covered in plastic wrap on a white marbled background.

Step 4. Cover and chill the cookie dough in the refrigerator while you make the cupcakes and frosting.

Recipe tip: You’ll likely have leftover edible cookie dough. Store it in a sealed container in the fridge for up to a week — it’s great on ice cream or enjoyed on its own.

Small Batch Vanilla Cupcakes

Mixing vanilla cupcake batter in a large glass mixing bowl on a white marbled background.

Step 1. Combine the dry ingredients and butter, sugar, and egg in a mixer. Beat on medium-high until blended, scraping the bowl as needed.

Added milk and vanilla extract into vanilla cupcake batter in a large glass mixing bowl on a white marbled background.

Step 2. Add vanilla and milk and mix just until combined. The batter should be scoopable and slightly thin, not runny.

Metal cupcake tin with six filled cavities with vanilla cupcake batter on a white marbled background.

Step 3. Divide the batter evenly among six liners using a 1½ tablespoon scoop or similar tool.

Six vanilla cupcakes baked in a metal cupcake tin on a white marbled background.

Step 4. Bake at 350°F (177°C) for 18–20 minutes until golden and slightly domed. Cool completely before filling.

Chocolate Chip Cookie Dough Buttercream Frosting

Recipe tip: Use heat-treated flour in the buttercream as well. Do not substitute regular untreated flour for the frosting that will be eaten raw.

Light brown sugar, unsalted butter, and vanilla extract in a large glass mixing bowl on a white marbled background.

Step 1. Beat butter, brown sugar, and vanilla until smooth and creamy.

Heat treated all purpose flour, powdered sugar, and salt added to cookie dough buttercream mixture in a large glass mixing bowl.

Step 2. Add sifted powdered sugar, heat-treated flour, and a pinch of salt, mixing on low until combined.

Milk added to cookie dough buttercream mixture in a large glass mixing bowl.

Step 3. Add milk a tablespoon at a time until you reach your desired consistency; use two tablespoons for a softer frosting.

Mini semi sweet chocolate chips folded into cookie dough buttercream frosting in a large glass mixing bowl.

Step 4. Fold in mini semi-sweet chocolate chips and set aside in the fridge briefly if you want a firmer piping consistency.

Assembling the Chocolate Chip Cookie Dough Cupcakes

Vanilla cupcakes with centers cored out and filled with a small scoop of edible chocolate chip cookie dough on a white marbled background.

Step 1. Core a 1-inch center from each cupcake and press a small ball of chilled edible cookie dough into the cavity.

Chocolate chip cookie dough filled vanilla cupcakes topped with chocolate chip cookie dough buttercream frosting.

Step 2. Pipe or spread the cookie-dough buttercream on top and finish with a few mini chocolate chips. Serve and enjoy.

Helpful Tips

Don’t overmix the cupcake batter. Overmixing develops gluten and can create dense cupcakes. Mix until ingredients are just incorporated.

Use an oven thermometer. Oven temperatures vary; an oven thermometer ensures accurate baking temperature and more consistent results.

Storing your cupcakes. Unfilled vanilla cupcakes can be baked 2–3 days ahead and stored in an airtight container at room temperature. If the tops become slightly sticky, let them sit uncovered for 30 minutes before frosting.

In hot or humid conditions, refrigerate the cupcakes in a well-sealed container; chilling can dry them slightly, so plan accordingly.

Black and white ceramic dessert plate placed on a pink cloth napkin with six chocolate chip cookie dough cupcakes.

Recipe FAQs

What decorating tip did you use to pipe the buttercream?

A Wilton 1A (open circle) tip with a medium piping bag works well for the frosting, but you can use your preferred tip for different looks.

What liners did you use?

Wavy cupcake liners are used for the photos, which give a decorative edge. Any standard liner will work; just be mindful of the cookie dough center size.

Can I make these cupcakes in advance?

Yes. Make the components ahead and assemble before serving for the best texture and flavor.

What can I use to core out the cupcake center?

An apple corer works well. Alternatively use the wide end of a decorating tip or a small spoon to remove the center.

How large should the edible cookie dough centers be?

Keep them around 1 inch in diameter so the cupcakes don’t crack or split. You can make them longer in length if needed, but avoid larger diameters.

More Small Batch Cupcakes Recipes!

Small Batch Lemon Cupcakes

Small Batch Black Bottom Cupcakes

Small Batch Vanilla Cupcakes

Small Batch Chocolate Cupcakes

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