In a large pot, cook bacon over medium heat until crisp. Remove bacon and set aside, leaving drippings in the pot.
Add onion and celery to the pot; cook until onion is translucent.
Stir in potatoes, clam juice, and thyme. Bring to a boil, then reduce heat and simmer until potatoes are tender.
In a separate saucepan, melt butter over medium heat. Stir in flour until smooth. Gradually whisk in cream until thickened.
Stir cream mixture into the pot of chowder. Add clams and bacon. Season with salt and pepper to taste. Simmer for a few more minutes until heated through.