In a Dutch oven or soup kettle, combine the first five ingredients; bring to a boil.
Reduce heat; cover and simmer for 20 minutes or until vegetables are very tender.
With a potato masher, mash vegetables several times. Add bacon; continue to simmer.
Meanwhile, melt butter in a small saucepan; stir in the flour and cook, stirring constantly, for 1 minute.
Gradually whisk in milk. Bring to a boil; boil and stir for 2 minutes (mixture will be thick). Add vegetable mixture, stirring constantly.
Remove from the heat; add cheese and pepper. Stir just until cheese is melted