In a large pot or Dutch oven, cook bacon until crispy. Remove bacon and set aside, reserving 2 tablespoons of bacon fat.
Melt butter in the pot with the reserved bacon fat. Add onion and celery and cook until softened, about 5-7 minutes.
Add potatoes and clam juice to the pot. Bring to a boil, then reduce heat and simmer for 15-20 minutes, or until potatoes are tender.
In a separate bowl, whisk together heavy cream, thyme, and pepper. Gradually whisk into the chowder.
Stir in flour and cook for 1-2 minutes, until slightly thickened.
Add clams and cook for 5-10 minutes, or until heated through.
Crumble bacon over the chowder before serving.