Melt butter in a large saucepan over medium-high heat. Cook vegan bacon over medium heat, stirring occasionally, until lightly browned, about 12 minutes.

Add onions and garlic and sauté until translucent, about eight minutes. Scatter flour over the onions and sauté, stirring to incorporate, for two minutes; reduce heat if flour starts to brown.

Add tomatoes, stock, salt, pepper, bay leaves, thyme and heavy cream. Bring to a boil over high heat, then reduce to a gentle simmer over medium-low. Simmer for 30 minutes to allow flavors to meld.

Discard bay leaves and thyme. Let soup cool.

Working in batches, ladle soup into a blender and purée until smooth. (Alternatively, use an immersion blender.) Pass soup through a fine-mesh strainer into a clean saucepan. Taste and season with more salt as needed. Reheat, if desired. Soup can be stored in an airtight container in the fridge for up to one week or frozen for up to two months.