Preheat oven to 400 degrees. Place squash halves in a 9×13 baking dish, cut side down. Bake for 35 minutes.
Meanwhile, prepare the filling. Heat a large pot with the olive oil over medium-high heat. Add chopped onion and cook until translucent (about 3 minutes). Add garlic, cook for one minute then add the bulgur and red quinoa. Stir until combined. Pour in your vegetable broth and bring to a boil. Place lid on pot and reduce heat to simmer for about 15 minutes.
When the acorn squash is finished baking, scoop out the most of the flesh, leaving enough on the sides to keep the shell intact.
When quinoa is finished cooking, fluff with a fork. Add the squash flesh, cinnamon, nutmeg, salt, almonds and cilantro to the pot and stir until combined.
Add the filling back into the acorn squash and bake for 15 minutes. Enjoy!
Note: to make this dish more FODMAP-friendly, omit garlic and onion.