Preheat oven to 375°F. Cut a thin slice off the top of each bread boule. Hollow out the inside, leaving a 1/2-inch thick shell. Reserve the bread tops and inner bread for another use (like croutons). Place bread bowls on a baking sheet and bake for 10 minutes until lightly toasted. Set aside.
In a large pot or Dutch oven over medium heat, cook the bacon until crispy, about 5 minutes. Remove bacon with a slotted spoon and set aside, leaving the drippings in the pot.
Add butter to the pot. Once melted, add onion and celery; cook until softened, about 5 minutes. Add garlic and cook for 1 minute.
Sprinkle flour over the vegetables and stir to coat. Cook for 2 minutes, stirring constantly.
Gradually whisk in clam juice, heavy cream, and milk. Add the reserved clam juice from the cans. Bring to a simmer, stirring occasionally.
Add potatoes, bay leaf, and thyme. Reduce heat to low, cover, and simmer until potatoes are tender, about 15 minutes.
Stir in the chopped clams and cooked bacon. Season with salt and pepper to taste. Remove bay leaf.
Ladle the chowder into the toasted bread bowls. Garnish with fresh parsley and serve immediately.
Tips
For a thicker chowder, mash some of the potatoes against the side of the pot before adding clams.
If you can't find clam juice, substitute with bottled clam juice or use water plus an extra can of clams with their juice.
Bread bowls can be made ahead and stored in an airtight container for up to 2 days. Reheat in a 350°F oven for 5 minutes before filling.