Amorphous MoSx is a highly active, earth-abundant catalyst for the electrochemical hydrogen evolution reaction. Previous studies have revealed that this material initially has a composition of MoS3, but after electrochemical activation, the surface is reduced to form an active phase resembling MoS2 in composition and chemical state. However, structural changes in the MoSx catalyst and the mechanism of the activation process remain poorly understood. In this study, we employ transmission electron microscopy (TEM) to image amorphous MoSx catalysts activated under two hydrogen-rich conditions: ex situ in an electrochemical cell and in situ in an environmental TEM. For the first time, we directly observe the formation of crystalline domains in the MoSx catalyst after both activation procedures as well as spatially localized changes in the chemical state detected via electron energy loss spectroscopy. Using density functional theory calculations, we investigate the mechanisms for this phase transformation and find that the presence of hydrogen is critical for enabling the restructuring process. Our results suggest that the surface of the amorphous MoSx catalyst is dynamic: while the initial catalyst activation forms the primary active surface of amorphous MoS2, continued transformation to the crystalline phase during electrochemical operation could contribute to catalyst deactivation. These results have important implications for the application of this highly active electrocatalyst for sustainable H2 generation.