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In a large saucepan, cook the bacon over moderate heat until the fat is rendered and the bacon is crisp.
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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.
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Add half of the beer and cook until reduced by half.
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Add chicken broth and bring to a simmer.
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In a small skillet, melt the butter. Add the flour and cook over moderate heat, stirring, until lightly browned.
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Whisk this roux into the soup until incorporated and bring to a simmer. Cook until thickened.
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Add the heavy cream, cheddar cheese and the remaining beer and simmer, stirring occasionally, until thick and creamy.
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Stir in the bacon and season with salt and pepper.