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Background Identification of disease-associated spectral alterations of oral squamous cell carcinoma (OSCC) and oral potentially malignant disorders (OPMD) is critical to improving patient outcomes. Protein structural changes in serum can be investigated using a minimally invasive, potential adjunctive analytical method. This preliminary, exploratory study aimed to explore the ability of attenuated total reflection–Fourier transform infrared (ATR-FTIR) spectroscopy to characterize disease-associated serum protein structural alterations in OSCC and OPMDs relative to healthy controls (HCs). Methods A laboratory-based analytical study was conducted using 110 serum samples from clinically and histopathologically confirmed cases: OSCC ( n  = 22), oral leukoplakia (OLK) ( n  = 22), oral lichen planus (OLP) ( n  = 22), oral submucous fibrosis (OSF) ( n  = 22), and HCs ( n  = 22). Spectral data were obtained with a FTIR over the 400–4000 cm⁻¹ range. Protein secondary structure alterations were analyzed using spectral deconvolution and Gaussian curve fitting. The relevance of specific wavenumbers was evaluated, and sensitivity and specificity were calculated to describe their ability to differentiate diseased groups from HCs in an exploratory manner. Results Alterations in the Amide I region were evident in serum samples from OSCC and OLK compared with controls, although no direct statistical comparison between disease groups was performed. Ten wavenumbers (1372, 1381, 1390, 1398, 1412, 1421, 1609, 1635, 1665, and 1683 cm⁻¹) showed statistically significant disease-associated differences between diseased groups and healthy controls. Among the evaluated spectral features, the wavenumber 1390 cm⁻¹ showed the highest sensitivity and specificity values for distinguishing OSCC from HCs (77.3% sensitivity, 86.4% specificity) and OLK from HCs (86.4% sensitivity, 77.3% specificity). Conclusions ATR-FTIR spectroscopy revealed distinct protein structural alterations in serum samples from patients with OSCC and OPMD when compared with healthy individuals. Specific spectral features, particularly at 1381 cm⁻¹ and 1683 cm⁻¹, demonstrated consistent disease-associated alterations compared with HCs, indicating their potential utility as minimally invasive serum-based spectral markers in exploratory studies of oral cancer and OPMD.