The incidence of esophageal adenocarcinoma (EAC) has increased in recent years, whilst the five-year survival rate remains low at ~15%. EAC is associated with altered lipid metabolism, with obesity as a major risk factor. Conversely, cholesterol-lowering statin drugs are protective and attenuate growth and malignant potential of EAC cells. MALDI and spectroscopy studies report changes in the lipid profiles of EAC tissue compared to healthy squamous epithelium however, the specific lipid metabolism pathways altered in EAC and its pre-cancerous condition called Barrett’s esophagus (BE) remain unclear. To study these pathways, we conducted mass spectrometry (MS) -based proteomics and lipidomics experiments on EAC, BE and healthy esophageal biopsies. Lipid and proteins were extracted from cell pellets using a biphasic MTBE/methanol method. Proteomic profiling was performed on a QE+ MS (Thermo). Untargeted discovery lipidomics experiments were performed on a 1290 Infinity II/6550 Q-TOF LC/MS system (Agilent) whilst targeted MRM experiments were performed on a 6490 Triple Quadrupole MS system. Combined analyses of proteomic and lipidomic alterations were performed to identify lipid metabolic pathways differentially expressed in EAC progression. Our results show that changes in the metabolism of the antioxidant plasmenyl lipids are associated with advanced disease stages. This is in agreement with the known mechanism of EAC development, as a result of chronic insults to the esophagus by acids, digestive enzymes and other sources of oxidative stress. These findings provide new insights in the roles of lipid metabolism in the development and prevention of BE and EAC.