Chocolate Chip Cookie Dough Cupcakes

Name: Chocolate Chip Cookie Dough Cupcakes
Prep time: 15 min
Cook time: 20 min
Total time: 35 min
Ingredients: 1/4 cup Unsalted Butter (room temperature); 1/4 cup Granulated Sugar; 2 tbsp Light Brown Sugar; 1/2 tsp Vanilla Extract; 1/2 cup Heat Treated All-Purpose Flour; 1/8 tsp Salt; 1 tbsp Whole Milk; 1/4 cup Mini Semi-Sweet Chocolate Chips; 2/3 cup All-Purpose Flour; 1/2 tsp Baking Powder; 1/8 tsp Salt; 1/4 cup Unsalted Butter (room temperature); 1/3 cup Granulated Sugar; 1 large Egg (room temperature); 1/2 tsp Vanilla Extract; 1/4 cup Whole Milk; 1/4 cup Unsalted Butter (room temperature); 1/4 cup Light Brown Sugar; 1 1/3 cup Sifted Powdered Sugar; 1/4 cup Heat Treated All-Purpose Flour; 1/8 tsp Salt; 1/2 tsp Vanilla Extract; 2 tbsp Whole Milk; 2 tbsp Mini Semi-Sweet Chocolate Chips

These Small Batch Chocolate Chip Cookie Dough Cupcakes are soft and fluffy vanilla cupcakes filled with edible chocolate chip cookie dough, and topped with a fantastic chocolate chip cookie dough buttercream frosting!

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

Why You’ll Love this Recipe

I’m excited to add these small batch chocolate chip cookie dough cupcakes to my recipe box! Each part of this recipe can be made in advance before assembling them. Using Wilton wave cupcake liners, this recipe yields 6 cupcakes.

For the cupcakes, I used my Small Batch Vanilla Cupcakes recipe, and the edible chocolate chip cookie dough is adapted from my Chocolate Covered Cookie Dough Hearts recipe! The chocolate chip cookie dough buttercream frosting is super easy to make and pairs perfectly with the cupcakes for the ultimate treat for cookie dough lovers!

For more small batch recipes, check out my Small Batch Chocolate Cupcakes, Small Batch Cinnamon Rolls, or my Small Batch Gluten-Free Peanut Butter Chocolate Chunk Cookies!

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 ingredients shown in the image below are used to make this small batch chocolate chip cookie dough cupcake recipe. Items noted in the bulleted list are key ingredients that need more explanation.

Heat-Treated All-Purpose Flour. You can buy heat-treated flour online (I have never been able to find it in stores) or you can heat-treat all-purpose flour in your oven (more on how to do this below). You will need heat-treated flour for the edible cookie dough and the buttercream frosting. Do NOT use refrigerated cookie dough from the grocery store.
Whole Milk. I used whole milk, but you can also use 1%, 2%, or fat-free.
Mini Semi-Sweet Chocolate Chips. I do not recommend using regular-size chocolate chips for this recipe, as they will be too large for the chocolate chip cookie dough and will make the frosting difficult to pipe or spread onto the cupcakes.

For quantities and instructions, please see the recipe card below.

Substitutions

I did not use any dairy, flour, or egg substitutes (for the cupcakes). The edible chocolate chip cookie dough does not contain eggs.

How to Heat Treat All-Purpose Flour

I know we’ve all sampled some raw cookie dough at least once, maybe several times, in our lives (and hey, we’re still here!). However, the FDA warns that harmful strains of E. coli can be found in raw flour; hence, heat-treat your all-purpose flour if you cannot find any locally or online.

To heat treat your flour, follow these steps:

Preheat your oven to 300ºF.
Spread the all-purpose flour needed for this chocolate chip cookie dough cupcake recipe (both the cookie dough and the buttercream) evenly onto a rimmed baking sheet.
Bake the all-purpose flour for 10 minutes, mixing it every 2-3 minutes, or until it reaches 160ºF with a digital food thermometer.
Remove from the oven and let cool completely before using. If any clumps form while baking, break them up using a fork. Cooling takes about 25-30 minutes. Keep the heat-treated flour stored in an airtight container.

How to Make the Recipe

Below is a brief overview of how to make these chocolate chip cookie dough cupcakes. For the full printable recipe, which can be made using US customary or metric measurements using the toggle switch, visit the recipe card below.

Recipe Tip: Start with the edible chocolate chip cookie dough first because it needs time to chill in the refrigerator while you make the rest of the recipe. You must use heat-treated flour for this part of the recipe.

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

Step 1. Mix the butter, sugars, and vanilla extract. Mix together until it’s light in color and fluffy in texture.

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

Step 2. Add in the heat-treated all-purpose flour, salt, and whole 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 in the fridge while you make the rest of the recipe.

Recipe Tip: You will have leftover edible chocolate chip cookie dough. Simply keep it refrigerated in a well-sealed container for up to a week. It’s perfect for an ice cream topping or to enjoy as-is! Careful, though, it’s addictive!

Small Batch Vanilla Cupcakes

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

Step 1. Add all ingredients except extract and milk to a large mixing bowl. Mix them all together at medium to high speed until well blended.

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

Step 2. Add in the extract and milk. Mix until just combined. The batter should be easily scoopable and on the thinner side, but not runny.

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

Step 3. Evenly divide the dough into the cupcake liners. I recommend using a 1 1/2 tablespoon-size cookie scoop.

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

Step 4. Bake for 18-20 minutes at 350ºF. They should be a nice golden yellow with a slight dome shape on top. Transfer to a cooling rack to cool completely.

Recipe Tip: You must use heat-treated all-purpose flour for this part of the recipe. Do NOT use regular, untreated all-purpose flour.

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

Step 1. Add the butter, light brown sugar, and vanilla extract together in a bowl. Mix 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 in the powdered sugar, heated treated all-purpose flour, and salt.

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

Step 3. Add in the whole milk. Start with just one tablespoon. If you prefer a softer, creamier frosting, use two tablespoons.

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

Step 4. Fold in the mini semi-sweet chocolate chips.

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 out the centers of each cupcake. Then fill each one with a small ball of the edible chocolate chip cookie dough.

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

Step 2. Top each cupcake with the chocolate chip cookie dough buttercream frosting and a few mini semi-sweet chocolate chips. Enjoy!

Helpful Tips

Don’t overmix the cupcake batter. Over-mixing can cause a whole slew of issues with your cupcakes as they bake. Dense, chewy cupcakes is one of them.

Use an oven thermometer. Every oven is different and may not calibrate to the correct temperature like you think it is. I discovered this with both my old oven and new oven. Both said it was preheated to the correct temperature, but the oven thermometer showed it was actually 100 degrees cooler. So, word to the wise, get yourself an oven thermometer to ensure your oven is heating to the correct temperature!

Storing your cupcakes. The vanilla cupcakes without the cookie dough frosting or cookie dough filling can be made 2-3 days in advance and kept in a tightly sealed storage container at room temperature.

If the tops feel slightly sticky to the touch after storing, let them sit out uncovered for about 30 minutes before adding the frosting.

If high heat or humidity is an issue where you live, you can keep them stored in the refrigerator. They do tend to dry out more this way, so make sure they are in a well-sealed container!

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 chocolate chip cookie dough buttercream?

I used the Wilton 1A decorating tip with a medium-sized piping bag. The Wilton 1A tip is also known as the open or open circle tip.

Who makes the wavy liners you used with these cupcakes?

I used the wavy cupcake liners from Wilton. I’ve used them with my Small Batch Vanilla Cupcakes and Small Batch Black Bottom Cupcakes recipes.

Can I make these cupcakes in advance?

Yes! You can make each part of this recipe in advance and assemble the cupcakes when ready.

What can I use to core out the center of each cupcake?

I used an apple corer, but you can also use the wide end of a large decorating tip or spoon.

How small should I make my edible chocolate chip cookie dough centers?

I would make them no more than 1 inch in diameter. Any bigger, and you’ll find (at least with these wave cupcake liners) the cupcakes will start to crack and split from the liners. The length, however, can be longer.