Small Batch Peanut Butter Chocolate Cookie Cups
This post may contain affiliate links. See the Disclosure Policy.
When chocolate, peanut butter, and cookies collide, I call this a dessert trifecta. These peanut butter chocolate filled cookie cups stuff whipped ganache with peanut butter into a chewy brown sugar cookie cup for an easy, pop-in-your-mouth delight. Often referred to as fudge puddles or filled cookies, the small batch of one dozen cookies can easily be adapted for any holiday or special occasion.
Much like all of my small batch cookie recipes, these cookie cups are easy, with a capital ‘E’. 8 ingredients, 1 bowl, and a simple mix. The cookies are soft, chewy, and the mini size will make you thankful you only have 12 to devour
I first saw the recipe on Taste of Home. And I’ll be honest, the main thing that attracted me to this cookie was the fudge filling. But as a recipe developer, I had to make my version of the tasty cookie. Ironically, the filling in my cookie is not fudge (feel free to swap in my creamy fudge small batch frosting), but the most decadent, fluffy, ganache flavored with peanut butter.
Let’s talk more about our love for chocolate + peanut butter. In a cookie, like the chocolate peanut butter almond flour cookies, creamy peanut butter fluff is sandwiched between two cookies. In a cupcake (my favorite), you can literally scoop chocolate peanut butter buttercream frosting on top of a small batch of peanut butter cupcakes. It’s like Halloween, Christmas, and my birthday, all year-long!
Let’s Make the Cookies

Add the butter and sugars to the mixing bowl of your stand mixer. Beat until light and creamy.

Add the egg yolk and extracts to the creamed butter. Beat until the egg yolk is mixed in.

Add the dry ingredients to the wet. Mix until no dry streaks remain.

Cover the bowl and refrigerate the dough for at least 1 hour.

Use a 1 tablespoon measuring spoon to portion the dough. Roll each portion into balls.

Press the balls into lightly greased mini muffin wells with the back of a 1 teaspoon measuring spoon.
Tip! Use the back of a teaspoon instead of your fingers to make the cookie ‘cups’. This way, the cups will all be the same size and hold the same amount of filling!

Bake the cookies for about 12 minutes. The centers will fill back in slightly as they bake. Use the teaspoon again to re-shape the ‘cups’.

Once the cookie cups are completely cool, fill with the chocolate peanut butter ganache filling.

Am I the only one who gets special requests to make special desserts for a partner’s work? I’d love to hear how you customized the cookie cups. Let’s chat in the comments below! 👇
Small Batch Peanut Butter Chocolate Cookie Cups
EQUIPMENT
- Mini Muffin Baking Pan
INGREDIENTS
Cookie Cups
- ¼ cup unsalted butter, room temperature
- 2 tablespoons organic cane sugar (or granulated sugar)
- 2 tablespoons light brown sugar
- 1 large egg yolk, room temperature
- ¼ teaspoon vanilla extract
- ¼ teaspoon almond extract (optional; see Notes)
- ¾ cup all-purpose flour
- ¼ teaspoon baking powder
- ¼ teaspoon salt
Peanut Butter Ganache Filling
- 2 ounces semi-sweet chocolate (baking bar recommended)
- 2 tablespoons unsalted butter
- ⅛ teaspoon salt
- ⅓ cup heavy cream
- ½ cup powdered sugar
- ½ teaspoon vanilla extract
- 2 tablespoons creamy peanut butter (regular peanut butter like Jif or Skippy)
- 1 to 2 tablespoons chopped peanuts or sprinkles (optional toppings)
INSTRUCTIONS
Peanut Butter Ganache Filling
- To coordinate the timing of the filling and the cookies, start with the ganache.
- Chop the chocolate bar into small chunks. Add the chocolate, butter, and salt to a medium mixing bowl.2 ounces semi-sweet chocolate, 2 tablespoons unsalted butter, 1/8 teaspoon salt
- In a small saucepan, heat the heavy cream until small bubbles form along the sides of the pan. Do not boil! Alternative – Heat the cream in the microwave in a liquid measuring cup in 30-second increments until warm.1/3 cup heavy cream
- Pour the warm cream over the chocolate and butter and let it sit for 3 to 5 minutes without stirring. This will allow the heat to distribute to all the chocolate pieces. Don't let it sit too long though. If the cream cools too much, the ganache may be separate and be grainy.
- With a whisk or spatula, stir the chocolate until smooth. Let the chocolate cool slightly at room temperature for 5 to 10 minutes. Then cover with plastic wrap and refrigerate for at least 1 hour. The chocolate needs time to chill and thicken. Otherwise, it probably won't whip properly.
- Next, start the cookies.
Cookie Cups
- Lightly grease 12 wells in a mini muffin pan.
- In the stand mixer mixing bowl (see Notes for using a small mixing bowl), add the butter and both sugars. Beat on medium high speed until light and creamy.1/4 cup unsalted butter, room temperature, 2 tablespoons organic cane sugar, 2 tablespoons light brown sugar
- Add the egg yolk, and vanilla and almond extract. Continue to beat on medium speed until the egg is well incorporated.1 large egg yolk, room temperature, 1/4 teaspoon vanilla extract, 1/4 teaspoon almond extract
- Sprinkle the flour, baking powder, and salt over the wet ingredients. Mix on medium speed until no dry streaks remain.3/4 cup all-purpose flour, 1/4 teaspoon baking powder, 1/4 teaspoon salt
- Cover the bowl and refrigerate the dough for at least 1 hour. This will give the dough time to hydrate and develop flavor.
- Preheat the oven to 350F degrees and adjust the oven rack to the middle position.
- Use a tablespoon measuring spoon to scoop the dough. Roll each into a ball and drop into the prepared muffin pan. Use the back of a 1 teaspoon measuring spoon to push each dough ball into the muffin wells and create a cup.
- Bake the cookies for 12 minutes, or until the tops are light golden brown. The cups you made with the teaspoon will fill back in slightly when baked. Place the pan on a wire cooling rack and immediately press the teaspoon back into the centers to re-make the cup. Cool the cookies in the pan for 5 minutes. Then carefully remove to cool on the wire rack completely. If the cookie cups aren't releasing from the pan, run a sharp knife or offset spatula along the sides of the cookie to release.
- Finish the ganache once the cookies are cool – Add the powdered sugar and vanilla to the chocolate ganache. Use a hand mixer to beat until it is fluffy and creamy. Add the peanut butter, and continue to beat until smooth.1/2 teaspoon vanilla extract, 1/2 cup powdered sugar, 2 tablespoons creamy peanut butter
- The frosting is ready to use immediately and can be piped into the cookie cups. I recommend piping to fill the cookie cups completely. Sprinkle the tops with chopped nuts or sprinkles. The cookie cups will be fine at room temperature for one day. Beyond that, I recommend refrigerating to keep the ganache fresh.1 to 2 tablespoons chopped peanuts or sprinkles
RECIPE NOTES
- Serving Size – This is a small batch recipe that can be doubled.
- Mixer – If you want to use your standard KitchenAid stand mixer, I recommend the smaller 3-quart mixing bowl to mix the dough properly. Otherwise, use your hand mixer with a medium mixing bowl.
- Almond Extract – Almond adds a lovely flavor to the cookies. You can omit it and use 1/2 teaspoon of vanilla extract.
- Ganache Filling – The ganache can be made ahead of time and refrigerated. It will firm as it chills. When ready to use, bring it to room temperature and mix again to make it fluffy.
- Other Cookie Cup Filling Options – Browse my frosting small batch recipes for other options – I recommend a thicker frosting vs. a glaze. The caramel dairy free frosting and the chocolate fudge frosting would be delicious alternatives!
- Freezing – Cookie dough: Freeze for up to 3 months. Wrap well in plastic wrap and place in a freezer bag. Thaw in the refrigerator. Baked cookies: Freeze for up to 3 months. Place the cookies gently in a freezer bag or container. Thaw at room temperature. I don’t recommend freezing filled cookie cups. Freezing will change the texture of the filling.
About the Author …
Hi, I’m Erin! With years of experience baking for two in my own small household, I know about the love for desserts without the leftovers. I’ve tested, written, and photographed every one of the 300+ recipes on my website. And even had some of my desserts featured on Taste of Home, The Spruce Eats, ELLE, Parade, and more! From traditional to gluten free desserts for two, I have the recipe for you.
Click here to learn more about me →