Metallic nanocrystals are pervasive in many applications, but rational control over their synthesis for desired applications is still difficult due to a lack of understanding of their complex formation mechanisms. The advent of liquid phase transmission electron microscopy (LP-TEM) enables direct imaging of nanocrystal formation in liquids at nanometer scale spatial resolutions in real time. In LP-TEM, the electron beam serves both as the imaging tool and the reducing agent of metal precursor solutions to form nanocrystals. The TEM beam and use of radical scavengers were investigated to establish a reproducible environment for in situ nanocrystal synthesis more representative of wet chemistry synthesis. Through systematic LP-TEM experiments, we have uncovered the effects of electron beam chemistry on the nucleation and growth kinetics of nanocrystals through scaling and reaction kinetic models. These experiments provided a direct calibration of LP-TEM electron beam chemistry and relate the microscope parameters to the chemical reactions involved in nanocrystal synthesis. LP-TEM imaging of silver nanocrystal nucleation showed domains of preferential heterogeneous nucleation on a topographically uniform but chemically patchy water-silicon nitride interface. Next, we demonstrated the self-assembly of 3D platinum supraparticles and uncovered the effects of electron beam and solution chemistry on the structures of nanocrystals. Through quantitative image analysis, we have discovered the self-assembly of nanocrystals was a diffusion-controlled particle attachment process and was mediated by a balance between van der Waals attraction and steric repulsion. Finally, we demonstrated synthesis of bimetallic alloy nanocrystals containing gold and copper with LP-TEM from an electron beam sensitive metal thiolate precursor complex. A range of electron beam synthesis conditions were successfully established that formed alloyed nanocrystals with similar composition and structure as nanocrystals synthesized by wet chemistry. The results of the study demonstrated the important role of capping ligands in facilitating alloy formation through the formation of prenucleation cluster intermediates that prevent inter-metal electron transfer by binding with metal salts to form metal ligand complexes.