The microwave isn’t really the culprit when it comes to rubbery melted cheese, says Robert L. Wolke, professor emeritus of chemistry at the University of Pittsburgh and author of What Einstein Told His Cook: Kitchen Science Explained. “The cheese was simply heated too hot or too long.”
When the temperature is too high or cheese is heated too long, its protein molecules tighten, and water and fat are forced out. This results in rubbery, greasy melted cheese, says Wolke.
Though the microwave isn’t the main cause, it can make the problem worse, says Dr. John A. Lucey, an associate professor in the University of Wisconsin–Madison’s Department of Food Science. “In a normal oven, the air is hot, and this helps form a crust or skin to hold in [oil and water], but in a microwave the air in the unit is unaffected by the microwave process, so no crust forms.” If you microwave cheese under less power and for a shorter time, then “this kind of problem can be minimized,” he says.
Wolke adds that once cheese gets to the rubbery stage, there’s no going back, so it’s always best to melt cheese with low heat, regardless of the cooking method. He also suggests shredding or cutting up the cheese to increase the surface area, which makes it melt faster and reduces the need for prolonged cooking.