Preheat the oven to 400°F. Line a sheet pan with parchment paper.

Caramelize the onions: Heat the olive oil in a large lidded skillet over medium heat until shimmering. Add the sliced onions and cook, stirring occasionally, until very soft and caramelized, 20 to 25 minutes, taking care not to burn (reduce heat to medium-low if needed). Add a splash of water if the onions brown too quickly.

Meanwhile, make the meatballs: Combine the beef, coconut aminos, salt, garlic powder, onion powder, and ground black pepper in a large bowl and mix well with a rubber spatula or clean hands. Use clean, lightly oiled hands to form the ground beef mixture into 20 balls (about 2 tablespoons each). Place the meatballs on the lined sheet pan, spaced them evenly apart.

Bake until lightly browned and fully cooked with an internal temperature of 165°F, 10 to 12 minutes.

Finish the skillet: Add the fresh garlic, thyme, salt, and ground black pepper to the pan with the caramelized onions and cook until fragrant, 1 to 2 minutes. Add the rice and toast, stirring frequently, until golden brown, 2 to 3 minutes. Pour in the broth, coconut aminos, and ½ cup of water and stir to combine. Bring the mixture to a simmer, then reduce the heat to medium-low. Cover and cook until the liquid is absorbed, and the rice is fluffy, stirring halfway through to prevent any sticking, 16 to 19 minutes. If the water has been fully absorbed before the rice is done cooking, add ½ cup water. If the liquid isn’t absorbing enough, turn the heat back to medium.

Reduce the heat to low, uncover, and place the cooked meatballs on top of the rice. Taste and add more salt if desired. Sprinkle the Gruyère all over the top. Cover and cook until the cheese is melted, 1 to 2 minutes. (Alternatively, transfer the pan, uncovered, to the oven and broil on high, until the cheese is melted, 1 to 2 minutes.)

Spoon the rice and meatballs onto four plates. Garnish with the chopped parsley.