Preheat the oven to 375ºF. Line a muffin pan with silicone liners or grease well.
In a medium bowl, mix the dry muffin ingredients until combined (coconut flour, baking soda, nutmeg, salt).
In a large, separate mixing bowl, combine the wet ingredients (eggs, vanilla, honey, ghee, applesauce, and berries).
Slowly add the dry ingredients to the wet, mixing in about 1/3 of the dry mixture at a time, until it is all well combined with no dry clumps remaining.
Spoon the batter into the pan, filling each muffin cup about 2/3 of the way. Top with a few extra berries.
In a small bowl, combine the topping ingredients. Place a small amount of the topping over each muffin cup, using your fingers to sprinkle it over.
Transfer to the oven and bake for 22 to 25 minutes, or until the topping is melted and the edges of each muffin are golden brown.
Allow the muffins to cool, and enjoy!