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Step 1
In a large pot over medium-low heat, cook the bacon until the fat is rendered and the cubes are crisp about 6-8 minutes. Using a slotted spoon, transfer the bacon to a paper towel-lined plate to soak up any excess oil.
Step 2
Reduce the heat to low and add the leeks, celery, jalapeño, garlic, and 1/2 teaspoon each salt and pepper to the bacon fat. Sauté until the veggies have softened, about 2 minutes, and then add in the flour. Cook, whisking often until the roux is a light golden color, about 2 minutes.
Step 3
Whisk in the beer, broth, and milk and bring to a simmer. Reduce the heat to medium-low and cook, stirring often, until the soup has thickened, about 10-12 minutes.
Step 4
Stir in the pepper jack, cheddar, smoked cheddar cheeses, Worcestershire, and the remaining salt and pepper. Cook for an additional 5 minutes, season to taste with salt and pepper, and thin the soup with the additional stock if necessary.
Step 5
Divide among bowls and garnish with the bacon, chives, and additional cracked pepper. Serve hot with crusty bread.