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front view of pile of salted chocolate chunk cookies with pecan flour on a white cake stand

Salted Chocolate Chunk Cookies with Toasted Pecan Flour

Finally, chocolate chunk cookies that are gluten free, grain free, and dairy free, but don't taste like it! Toasted pecan flour, dark chocolate chunks, pecan pieces, and flaked coconut all come together in swirl of irresistible, chunky cookie goodness. One of my all time favorite cookies!
Course Dessert
Cuisine American
Keyword chocolate, cookies, dairy free, Gluten free, grain free
Prep Time 20 minutes
Cook Time 15 minutes
Total Time 35 minutes
Servings 26 Cookies



  • Preheat the oven to 350 degrees. Spread all 4 cups of pecan halves evenly between two rimmed baking sheets and toast for 8-10 minutes.
  • Set 1 cup of the toasted pecans aside and pulse the remaining 3 cups in a food processor until they're the texture of coarse crumbs. I have a standard size food processor and find it best to pulse them in two batches. Do not overdo it or you'll have pecan butter!
  • Cream the palm shortening, sugars, and maple in a stand mixer. Add eggs and vanilla and continue to beat until smooth.
  • In a separate bowl, stir together the pecan flour, coconut flour, shredded coconut, baking soda, sea salt, and cinnamon. Add this mixture to the wet and stir with a wooden spoon until well combined.
  • Roughly chop the reserved pecan halves as well as the dark chocolate bars, then fold them into the batter.
  • Use a mini cookie scoop to transfer large, heaping scoops of the batter to a parchment linked baking sheet. (I fill the scoop about 150%). If needed, use your fingers to help smooth out any rough edges on the mounds of scooped batter.
  • Bake for 14-18 minutes, or until the surface is just begins to brown and is slightly firm to the touch. It may seem like they're not quite because the centers will still seem too soft, but they'll continue to firm up as they cool.
  • Remove cookies from the oven and immediately add a very light sprinkle of kosher salt. This is optional so if you're not a sea salt and chocolate fan, just skip this step.
  • Allow cookies to cool on pan for 10 minutes (I set a timer), then transfer to a wire rack to cool completely.


  • Toasting the pecans for the pecan flour is an absolute must for the flavor. It really only takes a few minutes longer, so don’t skip it! 
  • Don’t overbake these. You’ll be tempted to leave them in the oven longer because the center will feel a bit too soft but, I promise, they’ll firm up as they cool.
  • Cool on the pan for 10 minutes, then transfer to a wire rack to cool completely. This keeps the bottoms from getting soggy, as can happen with nut flour cookies. 
  • Feel free to sub milk chocolate, semi sweet, or a blend of chocolates in place of the dark chocolate. (Milk chocolate bars typically have dairy in the ingredients, so avoid these if you're dairy free)
  • Make sure you use heaping mini scoops – about 50% more batter than a level mini scoop. That’s the key to get nice, thick cookies with that moist, chocolaty middle!
  • The kosher salt sprinkle is optional.
  • You can freeze the batter or the baked cookies in zipper bag or airtight container.