Heat olive oil in a large pot over medium heat. Add chopped onion and cook for 4-5 minutes until softened. Add garlic and cook for 1 minute more until fragrant.
Reserve 1 cup of small broccoli florets and set aside. Add the remaining broccoli, white beans, and vegetable broth to the pot. Bring to a boil, then reduce heat and simmer for 12-15 minutes until broccoli is tender but still bright green.
Add the nutritional yeast, salt, pepper, and nutmeg. Use an immersion blender to puree the soup until smooth and creamy, or transfer to a blender in batches.
Return soup to pot if needed, add reserved broccoli florets, and simmer for 3-4 minutes until just tender. Taste and adjust seasonings before serving.