Melt the coconut oil in a large pot over medium heat and saute the onion and pepper until tender, about 8 minutes. Add in the water, potatoes, corn, thyme, and 2 teaspoons of salt. Bring the water to a boil, then cover and reduce the heat, simmering until the potatoes are fork-tender, about 25 to 30 minutes.
Use an immersion blender to blend the soup directly in the pot, leaving as much texture as you like. Alternatively, you can transfer half of the soup to a blender or food processor and blend until smooth, then add the blended soup back to the other half of the soup for a thick, chowder-like texture. Season with additional salt and black pepper to taste, then serve warm with chopped chives, if you like.
Leftovers can be stored in the fridge for up to 5 days. Enjoy!