Heat olive oil in a large stockpot over medium heat.
Add diced onion and sauté for 5 to 7 minutes until translucent and slightly caramelized.
Add minced garlic and cook for 60 seconds until fragrant.
Incorporate the butternut squash cubes, cannellini beans, salt, pepper, nutmeg, and thyme; stir to coat.
Pour in the vegetable broth, ensuring the squash is fully submerged. Bring the mixture to a rolling boil.
Reduce heat to low, cover, and simmer for 20 to 25 minutes or until the squash is fork-tender.
Remove the pot from heat and stir in the nutritional yeast.
Using an immersion blender, process the soup until a completely smooth, homogenous texture is achieved.
Return to low heat briefly to ensure uniform temperature and adjust seasoning as required before serving.