Pre-eclampsia (PE) is a serious pregnancy-related disorder and the leading cause of maternal and fetal mortality and morbidity worldwide. The etiology of PE is poorly understood and a definitive diagnosis is still lacking. Herein, we used synchrotron-FTIR microspectroscopy as a new analytical tool to investigate the molecular changes in the structure and intensity of lipids (spectral range 3050–2800 cm−1) and protein-carbonyl (spectral range 1855–1485 cm−1) components of the plasma and link them to the pathogenesis of the disease. In the lipid region, an increase in the CH2 and CH3 peaks intensity was noticed in PE group compared to normotensive pregnancy reflecting abnormalities in the lipid profile and a high level of LDL. Increased CH2/CH3 ratio and red shifts were observed in the lipid region in PE highlighting structural variations of lipids and transformation of conformation of lipid tails. In the protein-carbonyl region, a decrease in the amide I and II absorption signals in the plasma of PE compared to normotensive controls was evident, and a red shift was noticed in the amide I region reflecting conformational changes and rearrangement in the α-helix secondary structure of the protein. Moreover, malondialdehyde level and lipid carbonyl peak at 1743 cm−1 were higher and more intense in PE due to the oxidative stress condition in PE. Spectral analysis of plasma drop from PE revealed that lipid and protein components tend to concentrate more in the central region of the drop, and that the most intense wavenumber values for the lipid and amide I region in the plasma drop were very comparable to their analogous in plasma film. Taken together, the current work provides evidence of the promising role of synchrotron-FTIR microspectroscopy in providing a better understanding of the pathophysiology of PE.