In this study, we present surface‐enhanced Raman spectroscopy (SERS) investigations of five analogs of a novel group of N‐benzylamino(boronphenyl)methylphosphonic acids: N‐benzylamino‐(3‐boronphenyl)‐S‐methylphosphonic acid (m‐PhS), N‐benzylamino‐(4‐boronphenyl)‐S‐methylphosphonic acid (p‐PhS), N‐benzylamino‐(2‐boronphenyl)‐R‐methylphosphonic acid (o‐PhR), N‐benzylamino‐(3‐boronphenyl)‐R‐methylphosphonic acid (m‐PhR), and N‐benzylamino‐(4‐boronphenyl)‐R‐methylphosphonic acid (p‐PhR) deposited onto 10‐nm gold nanoparticles in an aqueous solution at physiological pH (pH = 7). In addition, for the p‐PhR molecule, the SERS spectra in the various conditions of pH levels of the solutions (from pH = 3 to 11) and phosphonic acid concentration (10−3–10−5 M) were measured. In general, the SERS spectral profiles indicate that at pH = 7, all of the aforementioned molecules interact with the colloidal gold surface via a boronphenyl ring. However, the orientation of the boronphenyl ring onto the substrate surface is different for each of the studied molecules. The boronic acid group of p‐PhS and p‐PhR binds to the gold nanoparticles, whereas the phosphonic acid group assists in the interaction with the substrate for p‐PhR only. For all the molecules, the –CLCα(P)N– fragment distinctly influences the molecule/gold interactions, especially in the case of o‐PhR. The previous differences in the compound behavior at the gold/liquid interface underline the role of an absolute configuration (–R and –S) and a type of isomer (orto‐, meta‐, and para‐) on the SERS signals, which means their influence on the adsorbate geometry. Additionally, based on the SERS results for p‐PhR in various environmental conditions, we draw conclusions about spectral changes (adsorbate geometry changes) as a result of the pH of solution and molecule concentration alternations. Copyright © 2014 John Wiley & Sons, Ltd.