Start by draining the canned clams, saving the juice. Chop the clams into small pieces, if desired, and set them aside.
In a large pot, cook the bacon over medium heat until crispy. Remove the bacon and set it aside, leaving the rendered fat in the pot.
In the same pot, add diced onions and garlic to the bacon fat, cooking until softened and fragrant (about 3-4 minutes).
Stir in the flour to create a roux, cooking for about 2 minutes to remove the raw flour taste.
Gradually add the reserved clam juice, followed by the milk and heavy cream, stirring constantly to combine and avoid lumps.
Toss in the diced potatoes, bring to a simmer, and cook until the potatoes are tender, about 15 minutes.
Stir in thyme, salt, and pepper to taste.
Add the chopped clams to the pot, and cook for an additional 5-7 minutes until heated through.
Crumble the cooked bacon and sprinkle it on top of the chowder for added flavor and crunch. Serve hot and enjoy!