These delicious chocolate peanut butter cookie cups are the perfect gluten-free dessert! Flourless peanut butter cookie cups are filled with a rich chocolate ganache that can easily be made low-carb for a keto-friendly treat.

a teal plate topped with several chocolate peanut butter cookie cups, sprinkled with sea salt

 

Peanut Butter Cookies with Chocolate Ganache

You are going to love these cute peanut butter cookies filled with a luscious chocolate ganache! After tasting how amazing these gluten-free and flourless cookie cups are in our Peanut Butter and Jelly Cookie Cups, we knew we had to try a version with chocolate!

These gluten-free cookie cups are based on one of our most popular recipes — Flourless Peanut Butter Chocolate Chip Cookies. You can easily make this recipe with a keto-friendly sweetener (like monk fruit) to keep this sweet treat low-carb and healthy. You’re going to want to make these again and again!

half of a chocolate peanut butter cookie cup in front of a plate full of the easy keto desserts

Why you’ll love this recipe:

  • Perfect for potlucks – These tiny treats are great for gatherings, potlucks, and kids’ parties as their small size make them great for sharing. Even if you plan to just try one, you’re going to want to keep eating them!
  • Easy to make ahead of time – These tasty cookies keep well in the fridge, perfect for prepping before parties and get-togethers! You can even freeze these and pull them out for unexpected guests or a surprise celebration.
  • Gluten-free, grain-free, & low-carb – These cookie cups use no flour at all, making them great for anyone sensitive to grains or gluten. Using monk fruit sweetener keeps these sugar-free and low-carb, great for keto! Feel free to use dairy-free and/or soy-free chocolate chips and a commercial egg replacement to make these super allergy friendly.
closeup view showing peanut butter cookie cups and low-carb chocolate ganache on a teal plate

Ingredients

Here’s a quick overview of what you’ll need for this easy dessert recipe. Find exact measurements in the printable recipe card at the bottom of the page.

  • Peanut butter – Creamy. If you’re keto, choose a version that doesn’t have any added sugars. I haven’t made this with almond butter, sunflower butter, or powdered peanut butter, but I do believe those substitutes could work.
  • Brown sugar sweetener and Vanilla extract – If you’re keto, use brown sugar monk fruit to keep these low-carb. Dark brown sugar gives you deeper sweetness than light brown sugar, but either can be used.
  • Baking powder and Salt – Provides lift and flavor to make sure the cookie cups have the right texture.
  • Egg – Large. I haven’t used an egg substitute, but store-bought egg replacements should work fine.
  • Chocolate chips and Heavy cream – If you’re keto, use Lily’s or another sugar-free brand of chocolate.
  • Optional: Sea salt, chocolate shavings, peanut butter drizzle, crushed peanuts, or sprinkles for finishing touches.

How to Make Chocolate Peanut Butter Cookie Cups

For this gluten-free dessert, you’ll need some heat-proof mixing bowls, mini muffin pan (highly recommend using silicone for easy removal), and a 1/2 teaspoon measuring spoon. Here’s a quick step-by-step guide to make these low-carb cookies.

Make the dough

Start by preheating the oven to 325 degrees F. If using a metal mini muffin pan, go ahead and line it with paper liners or grease it extremely well. Silicone pans are preferable as the cookie cups pop out perfectly without any effort.

In a mixing bowl, mix together the creamy peanut butter, sweetener, extract, baking powder, salt, and egg. Stir until a smooth peanut butter cookie dough batter forms. Scoop this dough into the pan, then form an indention into each bit of dough by pressing a 1/2 teaspoon measuring spoon into the center of each one.

Bake the cookie cups

Bake the cookies for 12-15 minutes until just set. You want to remove the cookies from the oven before they are completely finished (they should be set and no longer have a shiny appearance in the center of the cookie). The cookies will finish baking while they sit in the hot pan. Allow the cookies to cool for 7-10 minutes, then use the same measuring spoon (1/2 teaspoon is the perfect size) to repeat the indentions, creating the perfect little well in each cookie. Allow the cookies to finish cooling completely while you make the ganache.

Make the ganache

Finely chop the chocolate chips and place them in a heat-proof bowl. Warm up the heavy cream (microwave or saucepan is fine) until it is piping hot, then pour it over the chocolate. Cover the bowl with a lid or large plate and allow the chocolate to sit and melt for 2 minutes. After allowing it to melt, remove the cover and stir the chocolate until a smooth, creamy ganache forms.

Fill the cookies

gluten-free peanut butter cookie cups filled with sugar-free chocolate ganache in a mini muffin pan

Once the ganache is smooth and the cookies have cooled, carefully pour the ganache into each cookie cup and sprinkle the tops with sea salt, crushed peanuts, or other garnishes if desired.

How to serve Cookie Cups

We love these topped with a little sprinkle of sea salt to bring out the best flavors in the peanut butter and chocolate! If you want to put these over the top, add a drizzle of keto caramel sauce as well. With this keto ice cream, you can have a decadent low-carb dessert that would put any restaurant to shame!

More cookie cup filling ideas:

  • Chocolate ganache frosting – If you like a lighter, whipped filling with the same flavors, this airy filling is perfect for you.
  • Raspberry frosting – Pipe this fruity, creamy concoction into the cookie cups for a delicious version with a great spring or summer twist.
  • Vanilla cheesecake filling – This creamy filling would turn these cookie cups into mini cheesecake bites with a cookie crust!
  • Peanut butter fudge – Double down for your peanut butter lovers, and pour the warm fudge into the cookie cups, then let them cool before serving.
  • Whipped vanilla frosting – If you love the cream in a whoopie pie, this is the perfect recipe for you! It would be great in these peanut butter cookie cups.

Best way to store cookies with ganache

These cookies will last longest (about a week) when stored in an airtight container in the fridge. If kept at room temperature, the cookies will soften and may have a harder time staying together. To keep these even longer, skip the refrigerator and freeze in a single layer until solid (a few hours), then transfer to a freezer bag or container up to 2-3 months. Thaw overnight in the fridge.

More easy desserts:

  • Keto No Bake Cookies – These make a great low-carb, gluten-free, oat-free option for those missing out on those old fashioned no-bake chocolate peanut butter oatmeal cookies!
  • No Bake Peanut Butter Pie – This incredible recipe is the ultimate rich, decadent dessert to bring to any get-together! It’s also sugar-free and gluten-free, so everyone can enjoy.
  • Keto Peanut Butter Cheesecake Brownies – Rich and fudgy brownies have a luscious peanut butter cheesecake layer you’re going to love!
  • No Bake Peanut Butter Bars – You’ll get a great crunchy peanut texture combined with a smooth and creamy chocolate layer with this tasty, sweet snack.
  • Peanut Butter Balls – This keto dessert recipe is great for those who love the buckeye candy around the holidays!
a teal plate topped with several chocolate peanut butter cookie cups, sprinkled with sea salt

Get the Recipe: Chocolate Peanut Butter Cookie Cups

These delicious chocolate peanut butter cookie cups are the perfect gluten-free dessert! Flourless peanut butter cookie cups are filled with a rich chocolate ganache that can easily be made low-carb for a keto-friendly treat.
No ratings yet

Ingredients
 

  • 1 cup peanut butter
  • 1 cup brown sugar, brown sugar monkfruit if keto
  • 1 teaspoon pure vanilla extract
  • 1 teaspoon baking powder
  • 1/2 teaspoon salt
  • 1 large egg

Ganache Filling

  • 1/2 cup chocolate chips, sugar-free if keto
  • 1/2 cup heavy cream

Instructions
 

  • Preheat the oven to 325 degrees F.
  • Combine the peanut butter, sweetener, vanilla extract, baking powder, salt, and egg until a smooth cookie dough batter forms.
  • Scoop the dough into a 24-count mini muffin tin (this is much easier with a silicone pan. If using a metal pan, grease the pan well and/or line it with mini muffin liners)
  • Lightly press an indention with a 1/2 teaspoon measuring spoon.
  • Bake the cookies 12-15 minutes until set. note: remember, the cookies will finish baking on the hot pan once you remove them from the oven. They are done when they have set and no longer have a shiny appearance in the center of the cookie
  • Allow the cookies to cool for 7-10 minutes, and then use the same 1/2 teaspoon measuring spoon to gently make another indention in each cookie to create a perfect little well.
  • While the cookies are cooling completely, make the ganache.
  • Finely chop the chocolate chips and place in a heat proof bowl. Heat the heavy cream until it is piping hot and pour over the chocolate. Cover and allow the chocolate to sit 2 minutes.
  • Stir the chocolate until a smooth, creamy ganache forms.
  • Once the cookies have cooled completely, Add the ganache to each cookie cup and top with sea salt if desired.
  • Keep the cookies stored in an airtight container in the fridge.

Notes

When made with monk fruit sweetener and Lily’s chocolate chips, each cookie cup has just 2.2 net carbs.
Serving: 1 cookie cup, Calories: 85kcal, Carbohydrates: 2.8g, Protein: 2.8g, Fat: 7.5g, Cholesterol: 13.4mg, Sodium: 98.8mg, Fiber: 0.6g, Sugar: 1.3g
Did you make this recipe?Please leave a star rating and review below!