Cook Bacon: In a large pot or Dutch oven over medium heat, cook chopped bacon until crisp. Remove bacon with a slotted spoon and set aside, leaving the rendered fat in the pot.
Sauté Aromatics: Add onions and celery to the pot and sauté until softened, about 5–6 minutes. Add garlic and cook for 1 minute.
Add Potatoes and Flour: Stir in diced potatoes and sprinkle flour over the vegetables. Cook for 2 minutes, stirring constantly, to remove raw flour taste.
Add Liquid: Gradually stir in clam juice and reserved clam liquid. Bring to a simmer and cook until potatoes are tender, about 15–20 minutes.
Add Milk, Cream, and Clams: Reduce heat to low. Stir in milk, heavy cream, and chopped clams. Add thyme, salt, and pepper. Simmer gently for 5–7 minutes, ensuring chowder does not boil.
Finish with Bacon and Garnish: Stir in crispy bacon (reserve a small amount for topping). Adjust seasoning if necessary.
Serve: Ladle chowder into bowls, garnish with chopped parsley and reserved bacon. Serve with oyster crackers or crusty bread.