Elucidating the polyethyleneimine (PEI) chemistry to predictively and reproducibly synthesize gold nanoparticle (AuNP)-PEI conjugates with desired properties has been elusive despite evaluation in numerous studies and reported enhanced properties. The lack of reproducible methods to control the core size and stability has led to contradictory results for performance and safety; thus, advancement of the conjugate platform for commercial use has likely been hindered. Recently, we reported a robust, reproducible method for synthesizing PEI-functionalized AuNPs (Au-PEIs), providing an opportunity to investigate structure-function relationships and to further investigate synthesis parameters affecting performance, where only materials stable in biological media are candidates for use. The properties of Au-PEIs prepared by the optimized reduction of HAuCl4 using four different structural variants of PEI changed significantly with the PEI molar mass and backbone form (branched or linear). In the present study using our previously reported synthesis procedure, comprehensive analysis of properties such as size distribution, surface plasmon resonance (SPR), morphological state, surface functionality, and the shelf life has been systematically evaluated to elucidate the role of surface chemistry and reactive groups involved in conjugation, as a function of conjugate size and morphology. Being important for commercial adoption, the chemistry was related to the observed colloidal stability of the product in relevant media, including exposure to physiological variables such as salt, pH, proteins, and thermal changes. Overall, this work advances progress toward smart design of engineered nanoscale drug delivery systems and devices by providing unreported details of contributions affecting formation, stability, and fate.