To a 5-quart Dutch oven over medium heat, add bacon strips, cut into 1 inch portions. Cook bacon fully and remove to a paper towel lined plate to drain of excess grease. Remove all but 2 Tablespoons of bacon fat from the Dutch oven.
Add the butter to the Dutch oven and melt. Add the diced onion and saute for about 5 minutes until tender and becoming translucent. Dust in the flour and stir for a minute to cook and thicken. Add the potatoes and toss. Pour in the clam juice from the bottle as well as the reserved clam juice from the cans. If more liquid is needed to cover the potatoes, add water or chicken stock.
Cover and boil about 15 minutes until potatoes are tender. Stir every few minutes to keep the bottom from burning and to check the potatoes for even cooking.
Clam chowder can be stored in an airtight container in the fridge for about 3 days. Do to the high amount of dairy, it’s not a good soup for freezing. Next day clam chowder is possibly better than the first day since the flavors have a chance to really develop. Just keep the bacon bits to the side for topping, otherwise they’ll become rubbery.