In a heavy-bottomed pot over medium heat, melt 1 tablespoon of ghee. Add the popcorn kernels and stir to coat.
Cover with a lid and wait for the popping to begin.
Meanwhile, into a small saucepan over low heat, melt the remaining 2 tablespoons of ghee. Add the maple syrup and sea salt. Stir to combine.
Once the popping has slowed down to a few seconds between each pop, open the lid and pour the maple mixture over the popcorn. Shake the pot to combine.
Finally, sprinkle nutritional yeast (if using) on top.