What makes soup separate?

Answer 1

In general, the liquid being used for the soup hasn't emulsified with the fats and/or other ingredients. That's the short answer. When making soup that may separate (that being, any soup that is meat-based), you should allow enough time for the soup to fully emulsify. If you try to make it quickly, the liquid won't have enough time to fully blend with other ingredients and you'll be left with heavier ingredients sinking, the liquid portion (broth, wine, beer, water) remaining below the fat layer which floats to the top. If that happens, plan on staying next to the stove and stir the soup constantly over low heat to force emulsification. You'll notice at some point that the liquid has become thicker; it's at this point that the meat and other ingredients have "become one" with the liquid. The soup may again separate if refrigerated but if you serve it the night you make it, you shouldn't notice any separation that detracts from the flavor and appearance of the soup.

If you're making a cream-based soup, you can force emulsification by creating a roux (a flour-based thickening) that will be added with other ingredients. The roux will act as the emulsifier and your liquid will become smooth and well-blended.