An accurate description of metal nanoparticle (NP)–support interactions is required for designing and optimizing NP catalytic systems because NP–support interactions may significantly impact NP stability and properties, such as catalytic activity. The ability to calculate NP interactions with amorphous supports, which are commonly used in industrial practice, is hampered because of a general lack of accurate atomically detailed model structures of amorphous surfaces. We have systematically studied relaxation processes of Pt₁₃ NPs on amorphous silica using recently developed realistic model amorphous silica surfaces. We have modeled the NP relaxation process in multiple steps: hard-sphere interactions were first used to generate initial placement of NPs on amorphous surfaces, then Pt–silica bonds were allowed to form, and finally both the NP and substrate were relaxed with density functional theory calculations. We find that the amorphous silica surface significantly impacts the morphology and electronic structure of the Pt clusters. Both NP energetics and charge transfer from NP to the support depend linearly on the number of Pt–silica bonds. Moreover, we find that the number of Pt–silica bonds is determined by the silica silanol number, which is a function of the silica pretreatment temperature. We predict that catalyst stability and electronic charge can be tuned via the pretreatment temperature of the support materials. The extent of support effects suggests that experiments aiming to measure the intrinsic catalytic properties of very small NPs on amorphous supports will fail because the measurable catalytic properties will depend critically on metal–support interactions. The magnitude of support effects highlights the need for explicitly including amorphous supports in atomistic studies.