Heat the oil in a large dutch oven or stockpot over medium heat. Once hot, add the garlic and onions and sauté for 2 - 3 minutes until the onions start to soften. Add the seasonings and squash and cook another 3 - 4 minutes until everything is super fragrant. Deglaze the pan with a splash of water as needed.
Stir in the beans, tomatoes, quinoa, broth, and water. Bring the mixture to a boil, reduce to simmer and cover for 30 minutes. Remove the lid and stir in the kale. Cover again and cook for another 5 - 10 minutes until the squash is tender.
Remove the pan from the heat and stir in the nutritional yeast and lemon juice. Allow to cool slightly, then taste and adjust seasonings as desired.
Serve hot with a sprinkle of red pepper flakes and a piece of crusty bread!