Per- and polyfluoroalkyl substances (PFAS) are environmental pollutants that have been associated with adverse health effects including liver damage, decreased vaccine responses, cancer, developmental toxicity, thyroid dysfunction, and elevated cholesterol. The specific molecular mechanisms impacted by PFAS exposure to cause these health effects remain poorly understood, however there is some evidence of lipid dysregulation. Thus, lipidomic studies that go beyond clinical triglyceride and cholesterol tests are greatly needed to investigate these perturbations. Here, we have utilized a platform coupling liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) separations to simultaneously evaluate PFAS bioaccumulation and lipid metabolism disruptions. For the study, liver samples collected from C57BL/6 mice exposed to either of the emerging PFAS hexafluoropropylene oxide dimer acid (HFPO-DA or "GenX") or Nafion byproduct 2 (NBP2) were assessed. Sex-specific differences in PFAS accumulation and liver size were observed for both PFAS, in addition to disturbed hepatic liver lipidomic profiles. Interestingly, GenX resulted in less hepatic bioaccumulation than NBP2 yet gave a higher number of significantly altered lipids when compared to the control group, implying that the accumulation of substances in the liver may not be a reliable measure of the substance's capacity to disrupt the liver's natural metabolic processes. Specifically, phosphatidylglycerols, phosphatidylinositols, and various specific fatty acyls were greatly impacted, indicating alteration of inflammation, oxidative stress, and cellular signaling processes due to emerging PFAS exposure. Overall, these results provide valuable insight into the liver bioaccumulation and molecular mechanisms of GenX- and NBP2-induced hepatotoxicity.