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Note: This recipe assumes that you have already premade butternut squash puree in advance. If you didn't, here are the step-by-step recipe and photos for making butternut squash puree from scratch. Or, if you are in a time crunch, just use store-bought canned pumpkin puree instead - it would work great here!
Bring a large pot of water to a boil. Add pasta shells and cook according to package instructions (usually 10 or 15 minutes). Drain. In the meantime, proceed with the recipe below.
Heat 1 tablespoon of olive oil on medium heat in a large oven-safe, heavy-bottomed, high-sided skillet. Add crumbled sausage and cook on medium heat for about 5 minutes or until the sausage is cooked. Drain excess fat.
To the same skillet with cooked sausage, add Italian seasoning, red pepper flakes, fresh spinach, and chopped fresh tomatoes (reserve some tomatoes for later use). Cook on medium heat, stirring frequently, for 4 or 5 minutes until the spinach wilts to your liking.
Remove the sausage and veggie mixture to a large bowl.
To the same, now empty, skillet, add 1.5 cups of butternut squash puree, 1 cup of heavy cream, and a small amount of fresh thyme over medium heat and stir to combine until the sauce reaches an even consistency. Remove from heat.
Preheat oven to 400 F.
After the pasta shells are cooked and drained, start stuffing each shell with a spoonful of sausage, spinach, and tomato mixture.
If you have remaining stuffing - mix it with the creamy butternut squash sauce in the skillet.
Place each stuffed shell in a circular pattern on top of the creamy butternut squash sauce in a skillet.
Top the shells with shredded Pepper Jack cheese and the remaining chopped cherry tomatoes.
Place the skillet in the oven, uncovered, and bake in the preheated oven at 400 F for about 10 or 15 minutes to warm up the stuffed shells and melt the cheese.