Prep: Preheat the oven to 350F and line a baking sheet with parchment paper.
Roast the Butternut Squash: Peel the squash and discard any seeds or pulp. Cut the squash into thin 1/2” slices and place on the lined baking sheet. Bake in the middle rack of the oven for 25 to 30 minutes, until the squash is easily pierced with a fork.
Mash the Squash: Transfer the squash to a bowl and mash well with a potato masher, until you have an even puree. You can also blend the squash in a food processor, but this will result in a slightly denser gnocchi. Add the olive oil, nutritional yeast, nutmeg, and salt to the puree and mix well.
Make the Dough: Place the flour in a large mound on a wooden cutting board; use your hands or a spoon to create a well in the center of the flour. Transfer the butternut puree to the center of the flour and begin to knead it into the dough. I prefer to use a bench scraper to begin kneading, then eventually switch to my hands. You should be left with a mostly smooth ball of dough that’s slightly sticky to the touch. If the dough is too sticky you can knead in more flour, but note that the gnocchi will become more dense with more kneading and flour. Cover the dough ball in plastic wrap and let rest for 15 minutes.
Form the Gnocchi: While you form the gnocchi, bring a large pot of generously salted water to a boil. Cut the dough into 4 even portions. Dust the cutting board with more flour, then roll out one portion of the dough into a smooth ~1/2” log. Use a bench scraper or sharp knife to cut 1/2” segments of dough off of the log to form each gnocchi. Transfer to a clean baking sheet, and repeat with the remaining 3 segments of dough, dusting with more flour as necessary.
Boil: Add the gnocchi to the boiling water (I cooked them all in one batch) and stir occasionally to prevent sticking. The gnocchi will rise to the top of the pot when they are finished cooking; this should take between 3 and 5 minutes.
Drain: Drain the gnocchi, but do not rinse. Proceed to make the sauce (below), or serve in the sauce of your choosing!