Understanding ligand binding on silver nanoparticles (AgNPs) is crucial regarding its behavior in photocatalytical and bioanalytical applications. However, the preferentially adsorbed species on AgNPs and their relative binding affinities are uncertain when halide ligands are involved. Herein, we demonstrate the variations in the adsorbed species on citrate-reduced AgNPs upon ligand exchange to Cl − , Br − , and I − and propose a mechanism based on surface-enhanced Raman spectroscopy (SERS) results. When Cl − is introduced to the AgNPs, citrate anion desorbs, but its decomposition product, acetoacetate (AAc − ), is relatively preferred for coadsorption. When the halide ligands are bulkier (Br − or I − ), AAc − is also displaced due to stronger repulsion, while residual anionic surfactants (AS) can bind to the AgNPs presumably through the gaps between the bulky halide ions. Further, the above-mentioned coadsorbed species are present together with a cationic protein (type I collagen). AS persist in their coadsorption when I − ligands coat the AgNPs, resulting in the interference SERS spectra of AS overlapping with collagen. In contrast, collagen outperforms AS on Br − ligand coated AgNPs, and thus, no interference was observed. This study will bring attention to the potential pitfalls during precise surface functionalization of AgNPs or other plasmonic nanostructures for interfacial properties and applications.