Preheat oven to 400° F.
Place cubed butternut squash on a parchment-lined baking sheet. Add olive oil and use your hands to evenly coat the squash. Season with salt and pepper.
Roast butternut squash for 40 minutes, stirring once halfway.
After the squash has been cooking for 10-15 minutes, start the risotto by warming the vegetable broth in a pot over medium heat. This will allow the squash to be done approximately at the same time as the rice.
While broth is warming, heat olive oil in a wide pan.
Add the onion and cook over medium heat until translucent, about 2-3 minutes.
Stir in the thyme and cook for 1 more minute.
Add the Arborio rice and stir until it is well coated.
Add the wine and stir constantly until it is absorbed.
Once wine is absorbed, add one ladleful (approximately ¼ cup) of broth. Stir constantly until broth is absorbed.
Continue to add one ladleful of broth at a time to the rice as it is absorbed, stirring constantly, until rice is just tender and has a creamy consistency (will take about 20-25 minutes minutes from this point).
Once the rice is creamy and you have used all or most of your broth (you might not need it all), stir in the nutritional yeast and vegan Parmesan.
Once the Parmesan has melted, turn off the heat. Taste and add salt if desired.
Fold in the butternut squash. Serve immediately.