In a large sauce pan or soup pot, cook the bacon over medium-high heat until bacon is crispy, about 7 minutes. Using a slotted spoon transfer the bacon to a paper towel lined plate. Drain off all but 1-2 tablespoons of bacon fat.
Add the onion, bell pepper, jalapeño and thyme and cook until vegetables are tender, about 5 minutes.
Reduce heat to medium and add the butter, stirring until completely melted.
Sprinkle the flour over the vegetables and stir until the flour is fully incorporated. After the flour is incorporated add the beer, stirring constantly until it the mixture thickens.
Slowly add the chicken stock and cream and stir until completely combined. Bring to a low simmer.
Add the grated cheese a handful at a time until melted.
Salt and pepper to taste and add in half of the cooked bacon.
Garnish with additional bacon, chives or flat leaf parsley if desired.
