Drain the clams over a bowl and reserve the juice. Chop the clams smaller if desired and set aside.
In a large pot, cook the bacon over medium heat until crispy. Remove with a slotted spoon and set aside, leaving the fat in the pot.
Add the butter to the bacon fat, then the onion and garlic. Cook 3–4 minutes until soft and fragrant.
Stir in the flour and cook 2 minutes, stirring constantly, to form a roux.
Slowly whisk in the reserved clam juice, then the milk and heavy cream, stirring until smooth.
Add the potatoes, bring to a gentle simmer, and cook about 15 minutes until tender. Stir in the thyme, salt, and pepper.
Add the chopped clams and simmer 5–7 minutes until heated through. Do not boil.
Ladle into bowls, top with crispy bacon, and serve hot.