Semi-hard cheeses can be characterized by their bubbles, or “eyes”, whose growth mechanisms have generally been explained empirically. The objective was to design a relevant multi-scale investigation strategy in order to determine if there is a relationship between eye growth kinetics and surrounding cheese microstructure. Magnetic resonance imaging provided the spatial distribution and growth kinetics of individual eyes during ripening. The eyes were smaller, less numerous and growing slower under the rind than in the center. Three microscopic techniques were combined to study cheese microstructure. Light microscopy showed horizontal curd grains with junctions unchanged during ripening. Confocal laser scanning microscopy revealed fat globules embedded in a continuous protein network in both zones and ages. Scanning electron microscopy showed a comparable porous protein network for all samples. No microstructure difference was found on the basis of sample location or age, but this study showed that bacteria repartition could participate to the opening gradient.