Fourier-transform infrared (FTIR) spectroscopy was used to investigate molecular differences among peritoneal, ovarian, bowel endometriosis phenotypes and control tissues. Peritoneal lesions showed the most pronounced spectral changes in CH-stretching (2800–3000 cm−1) and 1000–1500 cm−1 regions, indicating protein and lipid alterations. Bowel lesions exhibited moderate but significant deviations, particularly in protein- and nucleic acid-associated bands, while ovarian lesions displayed subtler differences with increased lipid-related CH-stretching. Principal component analysis distinguished all phenotypes from controls, with peritoneal clustering most distinct, bowel intermediate, and ovarian partially overlapping. Key discriminative regions included phosphate vibrations (1080–1100, 1240–1250 cm−1), CH2 bending (~1450 cm−1), amide I (~1650 cm−1), and amide II (~1540 cm−1). Decision tree analysis identified phenotype-specific markers: 988 cm−1 (ovarian), 1101 cm−1 (bowel), 1544 cm−1 (peritoneal). Marker intensity correlated with tumor size and clinical scores, strongest in ovarian lesions. These findings highlight phenotype-specific FTIR fingerprints, offering diagnostic and prognostic potential in endometriosis.