Preheat oven to 350 degrees F. Line a 12 cup muffin tin with paper muffin cups.
In a large bowl, combine almond flour, oats, cinnamon, nutmeg, baking soda, sea salt, and chocolate chips. Mix together.
In another large bowl, mix together EB eggs, melted butter, carrots, beets, maple syrup, and vanilla extract. Mix until well combined.
Combine dry ingredients into wet ingredient bowl and mix until batter is thick and well combined.
Spoon batter into muffin cups and place in preheated oven for 25-30 minutes. Muffins will be nicely browned on top and a toothpick inserted into the center of a muffin comes out clean.