Add bacon to a large pot over medium-high heat and cook until browned. Use a slotted spoon to remove bacon from pot and set aside on a plate lined with a paper towel.
Add onion to the same pot and cook for 3-5 minutes, or until tender. Sprinkle flour on top and cook, stirring continuously, for 1 minute.
Gradually mix in chicken broth until combined then add potatoes and bring to a boil. Reduce heat to low and let simmer for 20 minutes, or until potatoes are tender. When potatoes are tender, use a potato masher to mash up some of the potatoes for a thicker soup.
Add milk, yogurt, salt and pepper and stir to combine. Cook for a few minutes until heated through.
Top with cooked bacon, cheddar cheese and chives before serving.