Preheat oven to 375 degrees F.
Peel and cube a large sweet potato into 1 1/2-inch pieces. Fill a saucepan with the cubes and filtered water. Bring to a boil then cook until the sweet potatoes are tender to the fork, about 15-20 minutes. Drain in a mesh strainer and let cool. Mash the sweet potato and reserve 1 cup.
Mix together the dry ingredients: oat flour, sorghum flour, potato starch, baking powder, salt and fresh thyme in a small bowl. Set aside.
To make the applesauce, peel off the apple skin and cut the apple into smaller pieces. Discard the core. Add the apple pieces and a few tablespoons of water to a small mini-prep blender. Puree the applesauce until smooth.
In the bowl of a stand mixer, add the sweet potato mash and melted ghee. Mix together at medium speed until well blended. Add the homemade applesauce and raw cane sugar. Beat at medium for a few minutes so the ingredients are nicely incorporated.
Add the dry ingredients to the mixture in the stand alone mixer and beat at medium until well incorporated, about 3-4 minutes. Add in green onions and bacon. Beat gently.
Divide the batter into the wells of a 24-cup mini muffin tin. Bake for about 16 minutes or until a toothpick comes out clean. Let cook on a baking rack. Store in the fridge because the muffins contain meat.