In a large saucepan, cook the bacon over moderate heat until the fat is rendered and the bacon is crisp.
Transfer the bacon to a bowl. Add the celery, onion, jalapeño, garlic and thyme to the saucepan and cook over moderate heat, stirring, until softened.
Add half of the beer and cook until reduced by half.
In a small skillet, melt the butter. Add the flour and cook over moderate heat, stirring, until lightly browned.
Whisk this roux into the soup until incorporated and bring to a simmer. Cook until thickened.
Add the heavy cream, cheddar cheese and the remaining beer and simmer, stirring occasionally, until thick and creamy.