Preheat oven to 400 degrees. Line a small baking sheet with foil.
Brush the inside of the acorn squash with olive oil and place cut side down onto the prepared baking sheet.
Bake for 30 minutes, or until the squash has softened and turned golden brown around the edges. While the squash is baking, begin preparing the filling.
Heat a large skillet over medium. Add the ground sausage to the skillet and cook.
Once the sausage is cooked completely, add in the garlic and cook until fragrant.
Stir in spinach, mushrooms, and rice. Cook until spinach has wilted and mushrooms have softened, just a few minutes.
Season with salt and pepper. Then, spoon the mixture into each acorn squash half.
Reduce oven heat to 350 degrees and place the squash back into the oven. Cook for another 8 minutes.
Remove squash from oven and serve with a sprinkle of red pepper flakes, Parmesan cheese, and fresh thyme leaves.