This study explored changes in binding modes of the most common ligand, citrate on silver nanoparticles (AgNPs) using single-particle surface-enhanced Raman scattering (SPSERS). Single AgNPs of 50 ± 10 nm diameter anchored on clean glass slides were monitored using time-dependent SP-SERS with 632.8 nm excitation at 1.3 μW incident (0.5 μW absorbed) power per nanoparticle. We observed several distinct spectra of citrate during time-dependent SP-SERS. Analysis of 1400 spectra showed the existence of two major groups termed as favorable (F) and probable (P) spectra based on their likelihood of appearance and intensities. These distinct spectra corresponded to a multitude of binding modes, structures, and variants of photocatalyzed products of citrate on the surface of dynamically changing AgNPs. Density functional theory (DFT) simulations were performed to model the structures and binding modes of citrate on an Ag(111) surface, and corresponding Raman spectra were computed and compared with distinct spectral types. Experiments performed with deuterated (2,2,4,4-d4) citrate-capped AgNPs provided additional evidence to understand the shifts in vibrational features obtained in SP-SERS of citrate-capped AgNPs. These systematic analyses of time-dependent SP-SERS spectra may be used for the reconstruction and vibrational tomography (VT) of ligands at the single-particle level. The proposed VT approach is similar to sectioning an object through a multitude of orientations and reconstructing its three-dimensional structure, although the structures reconstructed here are molecular orientations. © 2021 American Chemical Society.