Add the sliced bacon to a cold sauté pan or stock pot and set it over medium heat. Cook the bacon, stirring occasionally, until crispy, around 8 minutes. Reserve 2 tablespoons of rendered bacon fat in the pan and transfer the cooked bacon to a plate lined with paper towel to absorb excess grease. Cover and set aside at room temperature.

Add the onions to the pan, season with a pinch of salt and cook, stirring and lifting any brown bits off the bottom of the pan, until soft and translucent, around 5 minutes. Add the garlic and arrowroot starch and cook, stirring, until the garlic is fragrant and the starch has turned golden brown, around 2 minutes. Add the chicken broth, potatoes, thyme leaves, bay leaves, water and ¼ teaspoon black pepper. Stir everything to distribute, raise the heat to medium-high, bring the liquid to a steady simmer and cook until the potatoes are completely fork-tender, around 15 minutes.

Discard the bay leaves and use an immersion blender to blend roughly ¾ of the soup until smooth, leaving some chunks of potato for texture. If using a regular blender, transfer all but 1 cup of potatoes to the blender and blend until smooth before returning it back to the pan. If the soup is too thick, adjust with more water or chicken broth. If the soup is too thin, blend more of the potatoes to thicken it further or continue to simmer the soup, allowing it to reduce in volume.

In a separate bowl, combine the yogurt with 1 cup of the hot broth and whisk to incorporate. Pour the yogurt mixture back into the pan and whisk to combine. Add ¾ of the shredded cheese and whisk until just incorporated. Taste the soup for seasoning and adjust with salt and pepper as desired.

To serve, ladle the soup into individual bowls. Garnish with shredded cheese, reserved bacon bits, sliced green onion, sliced jalapeño, and a dollop of Greek yogurt. Serve immediately.