Chocolate Almond Flour Protein Muffins with a little sea salt sprinkled on top sitting on a blue background.

Chocolate Almond Flour Protein Muffins

  • Author: Kristen Stevens
  • Prep Time: 10 mins
  • Cook Time: 20 mins
  • Total Time: 30 minutes
  • Yield: 12 muffins 1x
  • Category: Breakfast
  • Cuisine: American


Chocolate Almond Flour Protein Muffins that are healthy enough for the breakfast table and delicious enough for dessert. They’re a muffin recipe that is truly the best of both worlds.



  • 1/3 cup coconut sugar
  • 1/3 cup melted coconut oil
  • 4 large eggs
  • 1 tablespoon vanilla
  • 2 cups almond flour
  • 3/4 cup cocoa powder
  • 1/4 cup (4 scoops) Vital Proteins Mixed Berry Collagen Peptides (their unflavored version works, too!)
  • 2 teaspoons baking powder
  • 1/2 teaspoon sea salt
  • 1/2 cup hot tap water
  • 1/2 cup chopped dark chocolate or paleo chocolate chips
  • 1/2 cup chopped pecans
  • Optional: flaky sea salt to top the muffins


  1. Preheat your oven to 350 degrees. Line a 12-cup muffin tin with liners.
  2. Add the coconut sugar, coconut oil, eggs, and vanilla to a large bowl and beat with electric beaters.
  3. Add the almond flour, cocoa powder, Vital Proteins Collagen Peptides, baking powder, and sea salt and beat until just combined. Add the hot water and carefully beat it into the batter. Fold in the chocolate and pecans.
  4. Divide the batter between the lined muffin cups, filling them nearly to the top. For extra chocolaty muffins, top with a few chocolate chips or chunks.
  5. Bake the muffins for 12-20 minutes – see the guidelines below. Let the muffins cool for 5 minutes before removing them from the muffin tin. Optional: top with a little sprinkle of flaky sea salt.


Fudgy dessert muffins: 12-14 minutes. Soft and delicate muffins that hold their shape: 16-17 minutes. Firm muffins that hold their shape: 18-20 minutes.

To prevent the muffin liner from sticking, make sure to let the muffins cool completely before taking it off.