Start by cooking the chopped bacon in a large pot or Dutch oven over medium heat. Stir occasionally until the bacon turns crispy and golden. Remove the crispy bacon bits with a slotted spoon and set them aside on a plate lined with paper towels. Be sure to leave about a tablespoon of the bacon grease in the pot for added smoky flavor.
Add the chopped onion to the same pot, cooking it in the reserved bacon grease. Sauté for about 5 minutes, just until the onion softens and becomes fragrant. Stir in the minced garlic, salt, and pepper. Next, melt the butter in the pot, then sprinkle in the flour. Cook this roux for about a minute, stirring constantly to avoid lumps.
Slowly pour in the broth and apple cider, whisking as you go to blend everything smoothly. Add the sweet potato cubes to the pot and reduce the heat to medium-low. Cover partially and simmer for 15-20 minutes, or until the sweet potatoes are soft enough to mash.
Once the sweet potatoes are tender, use a potato masher to mash them directly in the pot. Mash as much or as little as you like, depending on how chunky or smooth you prefer your chowder. Lower the heat and stir in the milk, chopped chipotle, chili powder, smoked paprika, Greek yogurt, and shredded cheddar cheese. Stir well until the cheese melts completely and the chowder becomes creamy and smooth.
Now is the fun part! Ladle the chowder into bowls and top each one with crispy bacon, a sprinkle of fresh cilantro, and a few slices of green onion. For an extra cheesy touch, you can also add more shredded cheddar on top. Pair it with some fresh bread or crackers and enjoy this comforting dish!