We employ atomically resolved and element-specific scanning transmission electron microscopy (STEM) to visualize in situ and at the atomic scale the crystallization and restructuring processes of two-dimensional (2D) molybdenum disulfide (MoS2) films. To this end, we deposit a model heterostructure of thin amorphous MoS2 films onto freestanding graphene membranes used as high-resolution STEM supports. Notably, during STEM imaging the energy input from the scanning electron beam leads to beam-induced crystallization and restructuring of the amorphous MoS2 into crystalline MoS2 domains, thereby emulating widely used elevated temperature MoS2 synthesis and processing conditions. We thereby directly observe nucleation, growth, crystallization, and restructuring events in the evolving MoS2 films in situ and at the atomic scale. Our observations suggest that during MoS2 processing, various MoS2 polymorphs co-evolve in parallel and that these can dynamically transform into each other. We further highlight transitions from in-plane to out-of-plane crystallization of MoS2 layers, give indication of Mo and S diffusion species, and suggest that, in our system and depending on conditions, MoS2 crystallization can be influenced by a weak MoS2/graphene support epitaxy. Our atomic-scale in situ approach thereby visualizes multiple fundamental processes that underlie the varied MoS2 morphologies observed in previous ex situ growth and processing work. Our work introduces a general approach to in situ visualize at the atomic scale the growth and restructuring mechanisms of 2D transition-metal dichalcogenides and other 2D materials.