In a food processor, pulse onion with thyme until you have a fine onion mixture well combined with the thyme. In a large bowl, add in the onion mixture with the salt and pepper. Add in almond flour, egg, and beef. Mix by hand.
Scoop up a heaped soup spoon of meat mixture and roll into a meatball. This should produce 10-12 meatballs. Heat pan on medium-high, add 1 tbsp of oil, and add meatballs in once heated. Fry them until browned, approximately 2 minutes on each side, only turning the meatballs once they've started to brown. Once all the sides are browned, gently remove the meatballs from the pan (place on a plate and set aside).
Reduce heat to medium and add ghee (clarified butter). Let melt, and then add tapioca starch. Whisk together to make a roux, then slowly add chicken broth, whisking until fully incorporated.
Add coconut aminos and Dijon mustard then whisk. Let simmer for another 2-3 minutes. Add in coconut milk and continue whisking. Let simmer on medium heat for 2-3 minutes, adding salt and pepper to taste.
Gently add the meatballs back into the pan in order for them to finish cooking. Do not stir until they are finished cooking. Let simmer until sauce thickens, approximately 7-8 minutes. See note*
Serve with a generous dash of pepper and a sprinkle of thyme.