In a large pot cook the bacon until crispy and fat is rendered. Remove and set aside on paper towel to drain. Reserve some or all of the bacon fat in the pot.
Melt butter in the pot. Add onion and cook for 3 minutes until tender. Add garlic and cook for an additional minute. Add flour and stir cooking for an additional minute.
Add broth, clam juice, potatoes, pepper, salt, thyme, cayenne pepper, and bay leaf to the pot and stir. Bring to a boil and simmer covered for 15 minutes.
Add heavy cream, chopped clams and most of the bacon and stir to combine and heat through.
Serve with a garnish of chives and remaining bacon.