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close up of oozing peanut butter

Gluten Free Peanut Butter Cup Cookies

  • Author: thebananadiaries
  • Prep Time: 30
  • Cook Time: 10
  • Total Time: 40 minutes
  • Yield: 12 1x
  • Category: Dessert
  • Method: Baking


Gooey and chocolatey gluten free peanut butter cup cookies that are bursting with peanut butter and naturally gluten free, dairy free, and vegan!



Paleo Cookie Cup:

  • 1 1/2 cup cassava flour (or 2 cups regular flour or gluten free 1-to-1 baking flour)
  • 1/2 cup coconut oil, softened but still cold
  • 1/2 cup coconut sugar
  • 3 tbsp ground flaxseed with 7 tbsp water or 1/3 cup unsweetened applesauce
  • 2 tsp vanilla extract
  • 1/2 tsp sea salt
  • 3/4 cup chocolate chips

Peanut Butter Cup:

  • 1 cup chocolate chips (I recommend either Lily’s Sweets, Pascha Organic, or Enjoy Life)
  • 1/2 cup smooth unsweetened peanut butter (I recommend Woodstock or Santa Cruz)


Peanut Butter Cups:

  1. Make sure you have 12 mini cupcake liners in a mini cupcake tin.
  2. Melt the chocolate in a microwave safe bowl or via stovetop.
  3. Add about 1 tbsp of melted chocolate to each mini cupcake liner. Use a spoon to smooth the chocolate up the sides of the liner a little to create a pocket for the peanut butter.
  4. Place the tray into the freezer to chill for 10 minutes before adding the peanut butter. Once the chocolate has set, remove from the freezer and add 1 tsp of peanut butter per cup.
  5. Place the tray back into the freezer to set for 5 minutes. Then fill the rest of the cups with chocolate to cover the peanut butter. 
  6. Place the tray back into the freezer to set for 10 minutes. 
  7. When they’re set, move the tray to the fridge to chill as you prepare the chocolate chip cookie cups.

Chocolate Chip Cookie Cups:

  1. Preheat the oven to 350F and line a muffin tin with cupcake liners or spray the tin with olive oil or coconut oil.
  2. In a large bowl, use a hand mixer to beat together the coconut oil, coconut sugar, flaxseed egg (or applesauce), and vanilla.
  3. Sift in the flour and sea salt, and mix until it’s a sticky batter.
  4. Add in the chocolate chips and fold until the chocolate chips are evenly distributed.
  5. Take about 2 tbsp of dough and press it into the bottom of each cupcake tin or cupcake liner and create a cup-shape to fit the peanut butter cup into.
  6. Place the muffin tin into the fridge to chill for 10 minutes. Then place the tin into the oven to bake for 12 minutes or until the cookies are golden.
  7. Remove from the oven and let cool for 10 minutes before removing from the cupcake tin.
  8. When ready to assemble the cookie cups, lightly press one peanut butter cup into the center of each cookie cup, making sure the edges don’t crumble (so don’t press hard!).
  9. Store in the fridge to help keep from. Enjoy!


  • Serving Size:
  • Calories: 308
  • Sugar: 14.4 g
  • Sodium: 153.1 mg
  • Fat: 21.2 g
  • Carbohydrates: 28.8 g
  • Protein: 4.6 g
  • Cholesterol: 0 mg

Keywords: peanut butter cup cookies, gluten free peanut butter cup cookies, vegan peanut butter cups