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!


I'm excited to add this small batch chocolate chip cookie dough cupcakes recipe to my recipe box! Each part of this recipe can be made in advance of assembling them together. Using the Wilton wave cupcake liners, this recipe makes six cupcakes total.
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 cookie dough lover treat!
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!
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Ingredients Needed
Edible Chocolate Chip Cookie Dough
- 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 simply heat treat all-purpose flour in your oven (more on how to do this below). You will need this for the buttercream frosting too.
- Salt. A pinch to help round out the cookie dough flavor.
- Unsalted Butter. Room temperature is best before mixing everything together. You can use salted butter, but omit the salt that's called for in the recipe.
- Sugars. You will need both granulated sugar (or organic cane sugar) and light brown sugar. I get both from ALDI and especially love their organic light brown sugar. Besides adding flavor and a little moisture, it smells WONDERFUL. They seriously need to turn that into a scented candle.
- Vanilla Extract. Always the perfect flavor enhancer. Pure vanilla extract is best.
- Whole Milk. I used a lactose free whole milk, but you can also use 1%, 2%, or Fat Free.
- Mini Semi-Sweet Chocolate Chips. You will only need ¼ cup of the mini semi-sweet chocolate chips for the edible chocolate chip cookie dough. Having a 12 ounce bag on hand will come in handy though because you will also need them for your chocolate chip cookie dough buttercream frosting.
Please note, this recipe is for edible chocolate chip cookie dough only—do NOT use all-purpose flour that has not been heat treated first. Do NOT use the refrigerated cookie dough found in your grocery store either.
And one last note here, I don't recommend using the regular size chocolate chips for this recipe as they will be too big to use in the chocolate chip cookie dough and will make the frosting difficult to both pipe or spread onto the cupcakes.
Small Batch Vanilla Cupcakes
- All-Purpose Flour
- Baking Powder
- Salt
- Unsalted Butter
- Granulated Sugar
- An Egg
- Vanilla Extract
- Whole Milk
Small Batch Chocolate Chip Cookie Dough Buttercream Frosting
- Unsalted Butter
- Light Brown Sugar
- Powdered Sugar
- Heat Treated All-Purpose Flour
- Salt
- Vanilla Extract
- Whole Milk
- Mini Semi-Sweet Chocolate Chips
Substitutions
I did not use any dairy, flour, or egg (for the cupcakes) substitutes. The edible chocolate chip cookie dough does not contain eggs.
How to Heat Treat Flour
I know we've all sampled some raw cookie dough at least once, maybe several times, in our life (and hey, we're still here!). The FDA does warn us, however, that harmful strains of E. Coli can be found in raw flour, hence heat treating your all-purpose flour if you cannot find any local to you or online.
To heat treat your flour, follow these steps:
- Preheat your oven to 350ºF.
- Spread the amount of all-purpose flour needed for this chocolate chip cookie dough cupcake recipe (the cookie dough and buttercream) out evenly onto a rimmed baking sheet.
- Bake the all-purpose flour for 5 minutes or until the flour reads 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.

How to Make the Recipe
Step 1. Make the edible cookie dough. I like to start with this part of the cupcake recipe first because I like to chill it in the refrigerator while I make the rest of the recipe. You'll need to use heat-treated flour for this part of the recipe.
Side note: you will have extra of this 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 just enjoy as-is! Careful, though, it's addictive!
Step 2. Make the vanilla cupcakes. The method for making these small batch vanilla cupcakes is slightly different from how my other cupcakes recipes are made. Everything is mixed together with the exception of the vanilla extract and milk. Let them cool completely before coring out the centers to add the edible chocolate chip cookie dough and chocolate chip cookie dough buttercream frosting.
Step 3. Make the chocolate chip cookie dough buttercream frosting. This buttercream is easy to make, but note that you will need heat treated flour for this part of the recipe too. Do NOT use regular untreated flour.
Step 4. Assemble the cupcakes. Core out the centers, then fill each one with a small ball of the edible chocolate chip cookie dough. Top each cupcake with the chocolate chip cookie dough buttercream frosting. Then enjoy!

Helpful Cupcake-Making Tips
Make the edible chocolate chip cookie dough first. I find that making this first, then chilling until I'm ready to assemble the cupcakes helps keep the process moving.
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 a cookie scoop. To divide out the vanilla cupcake batter, I used a 1 ½ tablespoon size cookie scoop. Worked like a charm.
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 my oven when it said it was preheated to the correct temperature—the oven thermometer said it was actually 100 degrees cooler.
So, word to the wise, get yourself an oven thermometer to make sure 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 appear to be 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!

Recipe FAQs
I used the Wilton 1A decorating tip with a medium-sized piping bag. The Wilton 1A tip is also known as the open tip or open circle tip.
The liners I used for this small batch recipe are the wavy cupcake liners from Wilton. I've used them with my small batch vanilla cupcakes and small batch black bottom cupcakes recipes.
Yes! You can make each part of this recipe in advance and then assemble them when ready.
I used an apple corer tool, but you can also use the wide end of a large decorating tip or spoon.
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.
1. Preheat your oven to 350ºF.
2. Spread the amount of all-purpose flour needed for this chocolate chip cookie dough cupcake recipe (the cookie dough and buttercream) out evenly onto a rimmed baking sheet.
3. Bake the all-purpose flour for 5 minutes or until the flour reads 160ºF with a digital food thermometer.
4. 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.
Enjoy These Other Small Batch Cupcake Recipes!
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📖 Recipe

Chocolate Chip Cookie Dough Cupcakes
Author:Ingredients
Edible Chocolate Chip Cookie Dough
- ¼ cup Unsalted Butter (room temperature)
- ¼ cup Granulated Sugar
- 2 tablespoons Light Brown Sugar
- ½ teaspoon Vanilla Extract
- ½ cup Heat Treated All-Purpose Flour
- â…› teaspoon Salt
- 1 tablespoon Whole Milk
- ¼ cup Mini Semi-Sweet Chocolate Chips
Small Batch Vanilla Cupcakes
- â…” cup All-Purpose Flour
- ½ teaspoon Baking Powder
- â…› teaspoon Salt
- ¼ cup Unsalted Butter (room temperature)
- â…“ cup Granulated Sugar
- 1 Large Egg (room temperature)
- ½ teaspoon Vanilla Extract
- ¼ cup Whole Milk
Small Batch Chocolate Chip Cookie Dough Buttercream
- ¼ cup Unsalted Butter (room temperature)
- ¼ cup Light Brown Sugar
- 1 â…“ cup Sifted Powdered Sugar
- ¼ cup Heat Treated All-Purpose Flour
- â…› teaspoon Salt
- ½ teaspoon Vanilla Extract
- 2 tablespoons Whole Milk
- 2 tablespoons Mini Semi-Sweet Chocolate Chips
Instructions
Edible Chocolate Chip Cookie Dough
- Using your hand-held mixer or stand mixer fitted with a paddle attachment, cream together the unsalted butter, granulated sugar, light brown sugar, and vanilla until light and fluffy.¼ cup Unsalted Butter, ¼ cup Granulated Sugar, 2 tablespoons Light Brown Sugar, ½ teaspoon Vanilla Extract
- Add in the heat treated all-purpose flour, salt, and whole milk, mixing until just combined. If the cookie dough seems a little dry, you may add in ½-1 teaspoon of milk.½ cup Heat Treated All-Purpose Flour, ⅛ teaspoon Salt, 1 tablespoon Whole Milk
- Fold in the mini semi-sweet chocolate chips, then cover and chill in the fridge until ready to use.¼ cup Mini Semi-Sweet Chocolate Chips
Small Batch Vanilla Cupcakes
- Adjust your oven rack to the 2nd level position (just above center). Preheat your oven to 350ºF and line a cupcake tin with 6 cupcake liners. I placed mine in the middle section of the tin.
- Using your hand-held mixer or stand mixer fitted with a paddle attachment, mix together the all-purpose flour, baking powder, salt, unsalted butter, granulated sugar and egg on medium-high speed until well blended (about 1 minute). Scrape down the sides of the bowl as needed.⅔ cup All-Purpose Flour, ½ teaspoon Baking Powder, ⅛ teaspoon Salt, ¼ cup Unsalted Butter, ⅓ cup Granulated Sugar, 1 Large Egg
- Add in the vanilla extract and milk, and mix until just combined (about 30 seconds). The batter should be easily scoopable and on the thinner side, but not runny.½ teaspoon Vanilla Extract, ¼ cup Whole Milk
- Using a medium-size cookie scoop (or a serving spoon and regular size spoon), evenly divide the batter into the cupcake liners.
- Bake for 18-20 minutes at 350ºF. They should be a nice golden yellow color with a slight dome to the top.
- Cool the cupcakes in the tin for 5-10 minutes. Remove and allow to cool completely before filling with the chocolate chip cookie dough and topping with the chocolate chip cookie dough buttercream frosting.
Chocolate Chip Cookie Dough Buttercream Frosting
- Using a hand-held mixer or stand mixer fitted with the paddle attachment, beat the unsalted butter, light brown sugar, and vanilla extract on medium-high speed until smooth and creamy.¼ cup Unsalted Butter, ¼ cup Light Brown Sugar, ½ teaspoon Vanilla Extract
- Reduce the mixer speed to low and add in the sifted powdered sugar, heat treat all-purpose flour, and salt mixing until combined. Scrape down the sides of the bowl as needed.1 ⅓ cup Sifted Powdered Sugar, ¼ cup Heat Treated All-Purpose Flour, ⅛ teaspoon Salt
- Add in the whole milk starting with just 1 tablespoon. If you prefer a softer, creamier frosting, add in the 2nd tablespoon of milk. Fold in the mini semi-sweet chocolate chips.2 tablespoons Whole Milk, 2 tablespoons Mini Semi-Sweet Chocolate Chips
Assembling the Cupcakes
- Core out the center of each cupcake about 1 inch in diameter. Scoop and roll a little of the chocolate chip cookie dough into a 1 inch ball, then gently press it into the center of each cupcake.
- Fill a medium size piping bag fitted with the Wilton 1A decorating tip (or one of your choosing) and pipe the frosting onto the top of each cupcake. If desired, top with a few extra mini semi-sweet chocolate chips.
Nutrition
Nutritonal information provided above is an estimate only and will vary based on specific ingredients used.
Debbie says
Made these for a coworkers birthday and they were a big hit. Thank you for the recipe!