Heat olive oil in a large pot over medium heat. Add the chopped onion, carrots, and celery with a pinch of salt. Sauté for 6-8 minutes until the onions are soft and translucent.
Stir in the minced garlic and dried thyme, cooking for 1 minute until fragrant. Then add the diced tomatoes and cook for an additional 2 minutes.
Pour in the rinsed quinoa and vegetable broth. Add the bay leaves and red pepper flakes. Bring the mixture to a boil, then reduce the heat to a simmer and cook for 25 minutes.