Slice acorn squash and remove seeds. Place flesh-side down on a large baking sheet lined with parchment paper. Bake for an hour to an hour and 15 minutes.
Meanwhile, boil the quinoa according to package instructions; drain.
In a large sauté pan over low heat, toast the pecans in the 1 tsp olive oil. Stir frequently to avoid burning. Once they are toasted, remove from heat and set aside in a bowl.
In the same sauté pan, add the oil, onion and garlic. Sauté over medium heat until onions and garlic are translucent. Add apples, herbs and cinnamon. Sauté until apples are soft. Add the brown sugar, quinoa and pecans and stir over low heat until combined.
Remove squash from the oven. If desired, add some butter or oil to the squash, then add the apple quinoa filling mixture and serve.