Dice onion into small pieces. In a small skillet, heat 1 tablespoon of butter over medium-high heat. Add onion and saute until soft and translucent.
Place 1 tablespoon of butter inside your crockpot and turn it to high to heat up with the lid on.
Scrub the outside of your potatoes and chop into bite size pieces. Place in your crockpot with the sauteed onions.
Add chicken broth, salt, pepper, and thyme. Cover and cook on low for 6 hours or high for 4 hours. If you crockpot cooks faster or slower, adjust the times by an hour.
When there is 30 minutes left of cooking, whisk the milk and flour together and pour in your crockpot. Stir everything and cook for 30 more minutes.
Serve warm soup with shredded cheese, crumbled bacon and fresh chives.