Heat a large skillet over medium heat. Add diced bacon then cook until brown and crispy, about 6-8 minutes. Transfer bacon to a paper towel-lined plate.
Add garlic and shallot to the skillet with the bacon grease then saute 2-3 minutes or until fragrant, stirring frequently. Whisk in flour and dried sage until lightly browned, about 1 minute. Next, gradually whisk in the milk and butternut squash puree then bring mixture to a boil over medium heat. Once boiling, reduce heat to low and let mixture simmer, stirring occasionally, until reduced and thickened, about 4-6 minutes.
Stir in cooked pasta and cheese until melted. Season with salt and pepper (add more to taste, if needed).
Top with bacon and chives then enjoy!
Recipe Notes
*Sweet potato or pumpkin puree can be substitute.
To make recipe vegan: Use vegan pasta, nut milk, dairy-free cheese, and omit the bacon!