Add potatoes to a large pot and add enough water to cover. Add a pinch of salt to the pot and bring to a boil. Cook potatoes 20 minutes, until easily pierced with a fork. Drain.
While the potatoes are cooking, heat olive oil in a dutch oven or large pot over medium-high heat. Add onions and garlic and cook until the onions have softened, about 5 minutes. To the pot add the chicken stock, milk, chipotle peppers, cumin, coriander and the cooked potatoes. Bring to a boil, reduce heat to low, and simmer 10 minutes.
Transfer the mixture to a blender (or use an immersion blender), add the cheese, and process until smooth. Season to taste with salt and pepper.
In a small bowl mix together the bell peppers, cilantro and red onion. Add lime juice and season with salt and pepper, to taste.
To serve, ladle the soup into bowls and garnish with a dollop of the pepper mixture.