Peanut Butter Cookie Cups with Gooey Chocolate Filling

These Peanut Butter Cookie Cups are filled with a rich chocolate ganache and baked until golden. Served warm, the ganache oozes from the center for a gooey, irresistible treat—perfect for parties, holidays, or an everyday dessert.

stack of peanut butter cookie cups with pieces of chocolate around it on a white plate

If you love the classic peanut butter and chocolate combination, these cookie cups deliver that flavor in an elegant, handheld form. They bake up soft and slightly chewy with a creamy chocolate center that’s best enjoyed warm.

stack of cookie cups showing the cookie tops with the ganache on a white plate with pieces of chocolate

Ingredients for PB Cookie Cups with Ganache

These ingredients are pantry staples for most kitchens. Swap the chocolate type to suit your preference—semi-sweet, dark, or white chocolate all work well.

  • milk chocolate chips – you can substitute semi-sweet, dark, or white chocolate chips if desired.
  • heavy cream – use heavy cream so the chocolate melts smoothly into ganache.
  • all-purpose flour – the base for the cookie dough.
  • baking soda – helps the cookies rise slightly and keeps them tender.
  • salt – balances sweetness and enhances flavor.
  • butter – room temperature for easy creaming.
  • peanut butter – creamy is used here, but crunchy works if you prefer a nutty texture.
  • brown sugar – provides moisture and a chewy texture.
  • egg – large egg to bind the dough.
  • vanilla extract – adds depth; pure vanilla gives the best flavor.
plate with a cookie cup on it with chocolate coming out of it and chocolate bites around it

How to make Peanut Butter Cookie Cups

Prepare the ganache first so it has time to chill and firm up before assembling the cookie cups. Freeze the ganache scoops briefly so they hold their shape when placed inside the dough.

  • Whisk flour, baking soda, and salt in a bowl until combined.
  • In a separate bowl, beat room-temperature butter, peanut butter, and brown sugar until light and fluffy using a hand mixer.
  • Add the egg and vanilla extract, beating until incorporated.
  • Stir in the flour mixture until just combined; avoid overmixing.
  • Fill prepared, greased muffin tins halfway with cookie dough.
collage of photos showing the step-by-step photo process for the cookie cups

How to store Peanut Butter Cookie Cups

Store cookie cups in an airtight container at room temperature for up to 2 days because of the ganache. For longer storage, refrigerate for up to one week.

To enjoy the gooey center again, warm a cookie cup in the microwave for 5–15 seconds—just enough to soften the ganache without melting the cookie completely.

Can I freeze Peanut Butter Cookie Cups?

Yes. There are two convenient methods:

  • Freeze the unbaked cookie cups: Press dough into a greased muffin tin as if baking, then tap each cup out onto a parchment-lined sheet and freeze until firm. Keep the frozen dough cups in a freezer bag for up to 3 months. Bake from frozen—add 1–3 minutes to the bake time.
  • Freeze before assembling: Scoop dough over frozen ganache truffles on a parchment-lined sheet, press gently, and freeze until firm. Store in a freezer container for up to 3 months.

To freeze baked cookie cups: Cool completely, freeze on a parchment-lined sheet, then transfer to a container or bag. Freeze up to 1 month. If stacking, freeze in a single layer first so the soft centers don’t collapse under weight.

Substitute the ganache with a peanut butter cup? Absolutely—placing a mini peanut butter cup in each dough-lined muffin cup before baking is a tasty and easy alternative.

stack of cookie cups showing the cookie tops with the ganache on a white plate with pieces of chocolate

Peanut Butter Cookie Cups with Chocolate Filling

Author:
Miranda Couse
These Peanut Butter Cookie Cups are baked until golden and filled with a sweet chocolate ganache that spills out when served warm.
4.50 from 2 votes
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Prep Time
20
Cook Time
16
Chill Time
1
Total Time
1 hr 36 mins

Course Dessert
Cuisine American

Servings
18 cookie cups
Calories
295 kcal

Ingredients

Ganache

  • 1 1/2 cups milk chocolate chips
  • 1/2 cup heavy cream

Peanut Butter Cookies

  • 1 1/2 cups all-purpose flour
  • 1/2 teaspoon baking soda
  • 1/4 teaspoon salt
  • 1/2 cup butter room temperature
  • 1 cup light brown sugar packed
  • 3/4 cup creamy peanut butter
  • 1 large egg
  • 1 teaspoon vanilla extract

Instructions

Ganache

  • Place 1 1/2 cups milk chocolate chips in a heat-safe bowl.
  • Heat 1/2 cup heavy cream in a saucepan over medium heat until bubbles form at the edges and steam rises—do not boil.
  • Pour the hot cream over the chocolate chips and stir until smooth. Chill the ganache in the refrigerator until scoopable, about 1 hour.
  • Scoop the chilled ganache with a 1-tablespoon scoop, roll into balls, place on parchment, and freeze until firm.

Cookie Cups

  • Preheat oven to 350°F. Grease a muffin tin with nonstick spray.
  • Whisk together flour, baking soda, and salt in a bowl.
  • Beat 1/2 cup butter and 1 cup light brown sugar until light and fluffy. Add 3/4 cup peanut butter, 1 large egg, and 1 teaspoon vanilla; beat until combined.
  • Stir in the flour mixture until just combined. Fill each muffin cup just under halfway with dough.
  • Remove frozen ganache balls and cut each in half. Place a ganache half into each dough-filled cup, pressing down slightly but keeping the ganache from touching the tin.
  • Bake 16–18 minutes or until edges are golden. Let cool in the pan 5 minutes before transferring to a wire rack to cool completely.

Notes

Storage: Store in an airtight container in the refrigerator for up to 5 days.

Nutrition

Calories: 295kcal
|
Carbohydrates: 33 g
|
Protein: 5 g
|
Fat: 17 g

(Nutrition facts are estimates and not guaranteed. Consult a registered dietitian for specialized dietary guidance.)