Gluten-Free Peanut Butter Cookies with Fudge Filling - Danielle Walker

It’s been 95 years since a Hershey’s employee (named Harry Reese!) came up with the idea to mix chocolate and peanut butter. What a gift to the world, right?! If you ask me, peanut butter and chocolate just belong together. Since I love the combo, I’m always thinking about how to update a classic recipe or coming up with my own recipe including the two. These Gluten-Free Peanut Butter Cookies with Fudge Filling are just the thing when I want a small, but rich tasting treat. 

image of gluten-free peanut butter cookies with fudge filling stacked on each other on a counter

Chewy Peanut Butter Cookie Recipe 

I toyed with my peanut butter cookie recipe a lot over the years, but this is my favorite iteration. I tried no bake peanut butter cookies and different baking times. Like Goldilocks, I was trying to find the recipe that was “just right.” And I found that a super quick, 10-minute bake renders the cookies chewy and soft, but with the structure to make sandwiches with them. 

Tip: Make sure to use unsweetened, but salted nut or seed butter. If you use one with sweetener, this amount of maple syrup will make the cookies too sweet so you’d want to reduce the maple syrup. Using an unsalted version, you’d want to add 1/4 tsp of salt to the cookie batter. Or, once baked, you could sprinkle the tops of the cookies with a large flake salt like fleur de sel or Maldon.

image of gluten-free peanut butter cookies with fudge filling open faced on a counter top.

Marshmallow and Chocolate 

Unless you’re making s’mores you may not think of marshmallow and chocolate together. But here, the marshmallow gets mixed with dairy-free butter, dark chocolate chips, and a dash of dairy-free milk. This gives the fudge mixture a density and heft that makes it the perfect sandwich filling. Now it sounds strange, but you want your marshmallows to be stale for this recipe. That’s the element that gives the fudge filling the right texture. So, you can either make my gluten-free homemade marshmallows and let them hang out for a few days, or you can buy some. Bagged marshmallows can have all different degrees of softness, but I find Dandie’s brand to be pretty hard to begin with, so I recommend those for this recipe.  

image of gluten-free peanut butter fudge cookies on a baking rack on a counter

Peanut Butter Chocolate Fudge

The combination and assembly of these cookies is where they come alive! Once the cookies cool, give them a dollop of the fudge, make a sandwich, and then refrigerate. They hold best when they’re given about 2 hours in the fridge to fully set. If you can wait that long…Enjoy!

Easy Gluten-Free Cookies 

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Gluten-Free Tagalongs

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Real Deal Chocolate Chip Cookies

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Gluten-Free Cookie Recipe Roundup 

Watch me make these Gluten-Free Peanut Butter Cookies with Fudge Filling on Instagram!

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Gluten-Free Peanut Butter Cookies with Fudge Filling

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  • Author: Danielle
  • Prep Time: 10 minutes
  • Cook Time: 10 minutes
  • Total Time: 2 hours and 20 minutes
  • Yield: 12 cookies 1x
  • Category: Dessert
  • Method: Stovetop
  • Cuisine: American



Fudge Filling:

  • 8 ounces dark chocolate chips (I like Guittard or Hu chips)
  • 2 ounces marshmallows (if using homemade, stale is best! Leave them out at room temperature, uncovered, for 3 to 5 days. Then seal in a reusable container until ready to use, OR use store-bought Dandies brand which are already a bit stale)
  • 2 tablespoons dairy-free butter (such as Miyokos)
  • 2 tablespoons dairy-free milk, cashew or full-fat coconut milk work best 



  1. Preheat the oven to 350 degrees F.
  2. In a medium bowl, mix the peanut butter *or alternative nut butter*, maple syrup and coconut sugar, coconut flour, vanilla and egg until well combined. Spoon 1 tablespoon of the mixture about 1 inch apart onto a parchment lined baking sheet.
  3. Bake until golden around the edges, 10 minutes. Remove the tray and carefully flatten the hot cookie dough mounds with the tines of a fork, making a crosshatch pattern on the cookies.
  4. Return the cookies to the oven and bake an additional 2 to 4 minutes, until golden on edges. Transfer to racks to cool. Repeat with remaining dough.
  5. Meanwhile, gently melt the marshmallows, butter, and milk together in a small saucepan over low heat. Remove from the heat and stir in the chocolate until melted. 
  6. When the cookies are fully cooled, scoop 2 teaspoons fudge mixture onto one cookie and top with a second cookie to make a sandwich. Refrigerate until firm, about 2 hours.


Gluten-Free Peanut Butter Cookies with Fudge Filling

image of gluten-free peanut butter cookies with fudge filling stacked on each other on a counter


  1. Isabella says:

    Would chia or flax eggs work?

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