1. Set a fine-mesh strainer over a medium bowl. Pour the clams through the strainer and transfer them to a small bowl. Set the clams and strained juice aside..
2. Melt the butter in a medium saucepan over medium heat. Add the onion and bacon and cook, stirring occasionally, until the fat has rendered from the bacon and the onion has softened, about 8 minutes.
3. Add the garlic and thyme and cook, stirring occasionally, until fragrant, about 1 minute. Sprinkle in the flour and cook, stirring occasionally, until the raw flavor has cooked off, about 2 minutes.
4. While stirring constantly, slowly add the reserved strained clam juice and bottled clam juice. Bring to a boil, stirring occasionally and making sure to scrape the bottom and sides of the pan. Reduce the heat to medium low, add the potatoes, and bring to a simmer. Cook, stirring occasionally, until the potatoes are knife tender, about 15 minutes.
5. Stir in the cream and reserved clams and return to a simmer. Taste and season with salt and pepper as needed.