As the temperature rises, some of this water turns into steam.
That steam needs somewhere to go.
Normally, it escapes through tiny spaces in the food. However, when the cheese begins melting, it can form a flexible layer that traps some of the steam and air underneath.
The trapped gases expand as they heat.
Eventually, they push against the softened cheese and lift portions of its surface, creating visible bubbles.
This is similar in principle to the way steam can create pockets inside certain baked foods.
The difference is that cheese has a unique protein-and-fat structure that affects how those pockets form and how long they remain visible.
Why some pizzas bubble more than others
Two pizzas may look nearly identical before going into the oven, yet emerge with noticeably different surfaces.
One may have smooth, evenly melted cheese.
The other may be covered with little golden blisters.
This variation can result from differences in moisture content, cheese thickness, oven temperature, and the way heat reaches the toppings.
