They don't.
The cheese and crust are different structures, so their bubbles form through somewhat different processes.
Cheese bubbles usually involve a melting dairy network trapping expanding steam and air.
Crust bubbles involve gas pockets within pizza dough.
These pockets may develop through fermentation, mixing, shaping, and heating.
How dough bubbles form
During fermentation, yeast consumes available sugars and produces carbon dioxide.
Some of that gas becomes trapped within the dough's gluten network.
When the pizza enters the oven, trapped gases expand.
Water within the dough also produces steam.
These processes contribute to the characteristic airy structure of baked pizza crust.
In some areas, the dough may inflate into large blisters.
This is especially visible in pizzas with thin centers and puffy outer edges.
Why this distinction matters
If your main concern is large air pockets in the crust, adjusting dough preparation may help.
But if the bubbles are forming directly in the melted cheese, poking holes in the dough will not necessarily solve the problem.
