Prep your baking sheets: Preheat the oven to 350ºF (175ºC). Line two baking sheets with parchment paper or silicone baking mats. Place the marshmallow fluff in a disposable piping bag. Set aside.
Mix the Dry Ingredients: In a medium mixing bowl, whisk together 1 ¼ cups gluten-free flour blend, ½ teaspoon baking powder, ½ teaspoon baking soda, and ½ teaspoon kosher salt. Set aside.
Cream the Wet Ingredients: In a large mixing bowl, beat ½ cup unsalted butter, ½ cup creamy peanut butter, ⅔ cup packed light brown sugar, and ⅓ cup granulated sugar with an electric mixer for 2-3 minutes, until light and fluffy. Scrape down the sides as needed.
Add the Vanilla & Egg: Mix in 2 teaspoons pure vanilla extract and 1 large egg until fully combined.
Combine the Dough: Gradually mix in the dry ingredients, stirring until just combined and no flour streaks remain.
Chill the dough for 30 minutes.
Assemble the Fluffernutter Cookies: Using a #30 cookie scoop (about 2 tablespoons big), scoop dough into about half of the scoop.
Pipe or spoon 1 teaspoon marshmallow fluff (from the 1 cup total) into the center of the dough.
Scoop the remaining dough on top, fully covering the marshmallow fluff.
Release the cookie dough ball onto the prepared baking sheet, ensuring the marshmallow fluff stays inside. If the marshmallow fluff rises to the surface of the dough, place the dough ball so that the marshmallow fluff is facing upwards.
Bake: Place cookies 3 inches apart on the baking sheet (about 6 per sheet). Bake for 10-12 minutes, until the edges are just set.
Cool: Let cookies cool on the baking sheet for 5 minutes, then transfer to a wire rack to cool completely. The cookies taste better the longer they sit since the peanut butter flavor intensifies as they cool.