Metal nanoparticles are most commonly synthesized in solutions and are often capped by organic ligands. Since the properties of nanoparticles depend on their shapes and sizes, knowledge of the morphological stability of the nanoparticles is essential for sustained functionality in any given application. Here, using in situ transmission electron microscopy (TEM) and time-lapsed optical spectroscopy, we studied the effects of electron beam irradiation and hydroxyl ion (OH−) concentration on the morphological evolution of polyethylenimine (PEI)-conjugated gold nanoparticles. Multiple spherical Au nanoparticles can be equally sintered under electron irradiation. Due to the presence of PEI ligand, AuNPs in this study are immobilized well on the carbon support without any obvious 3D rotation during the coalescence process. From the measurements of the coalesced particle shapes as a function of time and electron beam dosage, we find that the gold nanoparticle morphological evolution rates increase with increasing dosage. More interestingly, with the introduction of OH− into the solution after synthesis, we observe aggregation of individual gold nanoparticles into branched structures and the formation of quasi two-dimensional Au nanoplates at higher OH− concentration. Our results enhance our understanding of the role of solution chemistry and electron beam irradiation on the morphological stability of metal nanoparticles capped with organic ligands.