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Prick potatoes with a fork all over. Microwave for 4-8 minutes or until tender. Cut open and set aside to cool.
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In a large saucepan, melt butter over medium heat. Add in onion and sauté until translucent.
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Stir in flour, thyme, and pepper. Slowly whisk in milk and broth until smooth. Cook and stir about 5 minutes on medium heat until it starts to bubble and thicken.
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In a medium bowl, scrape out the insides of the potatoes and mix well into the soup, slightly mashing the potatoes as needed.
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Once the soup is well combined, break apart the cheese slices and add to the pot. Keep stirring until the cheese is fully melted.
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Crisp bacon on a paper towel lined plate in the microwave for about 5 minutes. Divide the soup between bowls, top with cheddar cheese, sour cream, crumbled bacon, chives, and cracked black pepper.