Set a large pot over medium-high heat and add the butter. When the butter is melted, add the onions. Cook, stirring frequently for 2 minutes, until softened and fragrant.
Add garlic and continue cooking for an additional 30 seconds.
Whisk in the flour until incorporated; the mixture will be thick.
Gradually add the broth, whisking until the consistency is smooth.
Bring just to a boil, then reduce the heat to low.
Add the cream cheese, cheddar cheese, milk, and black pepper to the pot. Stir frequently until cheeses are melted.
Add the prepared mac and cheese, stirring to distribute throughout the soup.
Adjust seasoning to taste and serve hot.