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Step 1
Start by heating up a large pot of salted water over high heat until it's almost boiling. Then cover and lower the heat to keep it hot until ready to use.
Step 2
For the crispy sage, heat oil in a large skillet over medium-high heat until it's hot and shimmering. Now add the sage leaves in a single layer and fry for 15-20 seconds, then flip with tongs, and fry for another 15-20 until crisp, but not browned. The color should turn dark green. Transfer to a paper-towel-lined plate to absorb excess oil.
Step 3
For the sauce, wipe out the pan and place it back on the stove, and heat up oil over medium heat. Once hot, add the onions and a pinch of salt. Sauté until tender and slightly golden. About 4-6 minutes.
Step 4
Add the garlic, red pepper flakes, nutmeg, and thyme. Sauté for 30-60 seconds, until fragrant.
Step 5
Pour the broth into the pan, then add the cubed squash, salt, and pepper, now give it a good stir. Raise the heat to get things simmering, then lower the heat to maintain a medium simmer. Cover with a lid and cook until the squash is fork-tender, about 12-14 minutes. Remove from heat.
Step 6
While the squash is cooking, bring the pasta water to a boil, then add the spaghetti and cook until just shy of al dente, and according to package directions (usually around 8-9 minutes). Stir occasionally to prevent sticking. Once the pasta is cooked, reserve ½ cup of pasta water and set aside. Drain the pasta and drizzle with olive oil to prevent sticking.
Step 7
Now, carefully add the contents of the pan into a blender, along with the milk, nutritional yeast, and lemon juice. Blend on high until smooth. Now pour the mixture back into the pan over medium heat. Taste for seasoning and add more if needed.
Step 8
Add the pasta and gently toss to combine, then cook for 1-2 minutes more. If the sauce is too thick, you can start adding some of the pasta water until you've reached desired consistency. You may not need any or much at all.
Step 9
Remove from heat and toss with a few crumbled sage leaves and vegan parmesan (optional). Serve with the remaining sage leaves and more vegan parmesan if desired. Enjoy!