To develop bioconjugated materials, it is necessary to understand how the various elements present in a conjugate interact with one another. To gain insights into nanoparticle-capping agent-protein interactions, gold nanoparticles (AuNPs) measuring 30 nm in diameter were coated with different molecules bearing a thiol group: 3-mercaptopropionic acid, 6-mercaptohexanoic acid, and 11-mercaptoundecanoic acid. The covalent conjugation of AuNPs to the protein bovine serum albumin (BSA) via a cross-linker reaction with N-hydroxysuccinimide and 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide was systematically investigated under different reaction conditions with variation of the concentrations of the mercaptoalkyl carboxylic acid (MA) and BSA. All the products were analyzed by UV-vis spectroscopy, gel electrophoresis, and Raman spectroscopy in every modification step. From analysis of the UV-vis results, it is possible at low concentrations of MA to see strong coupling among AuNPs, observed when they are aggregated by KCl, which does not happen at higher concentration of MA, indicating an AuNP-to-MA ratio of 1:130,000 is best for bioconjugation purposes. Agarose gel electrophoresis, a classic technique for biomolecule characterization, indicated that BSA is capable of altering the mobility of AuNPs when it modifies completely the surface of AuNPs because of its high molecular mass (around 66 kDa). Principal component analysis of surface-enhanced Raman spectroscopy data was successfully used as a chemometric tool to assist the characterization of the nanoparticle modification with linker molecules in the absence and presence of different BSA concentrations, making it possible to clearly evaluate the gradual substitution/modification of AuNPs (1:13,000 < 1:65,000 < 1:130,000 AuNP-to-MA ratio) and the conjugation with BSA, which is homogenous at a concentration of 0.01 g L-1. Graphical abstract.