Prepare the squash: If time allows, thaw the frozen butternut squash for about 15 minutes before cooking to ensure even heating. If you’re in a hurry, you can use it straight from frozen, but cooking time may increase slightly.
Sauté the aromatics: Heat olive oil in a large saucepan over medium heat. Add diced onion and cook for 3-4 minutes until softened and translucent. Add minced garlic and cook for another 30 seconds until fragrant, being careful not to burn it.
Add the squash: Add the butternut squash to the pan and stir to combine with the onions and garlic. Cook for 2-3 minutes, stirring occasionally.
Add liquids and seasonings: Pour in the vegetable broth, then add nutritional yeast, nutmeg, sage, and thyme. Season with a pinch of salt and black pepper. Bring to a gentle simmer.
Simmer until tender: Cover and simmer for about 10 minutes, or until the butternut squash is completely soft and can be easily mashed with a fork. If using completely frozen squash, this may take 12-15 minutes.
Blend until smooth: Transfer the mixture to a blender or food processor and blend until completely smooth and creamy. Be careful when blending hot liquids—work in batches if necessary and allow steam to escape.
Finish the sauce: Return the blended sauce to the pan over low heat. Add lemon juice and adjust seasonings to taste. If the sauce is too thick, add a splash more vegetable broth until you reach your desired consistency.
Serve: Toss with freshly cooked pasta, reserving some pasta cooking water to thin the sauce if needed. Garnish with additional herbs, a drizzle of olive oil, or toasted pine nuts if desired.