The influence of High Intensity Pulsed Electric Fields (HIPEF) or Thermal Treatment (TT) on minerals and fatty acids of fruit juice-whole (FJ-WM) or skimmed milk (FJ-SM) beverages was assessed after processing and during chilled storage. Mineral profile of both beverages was characterized by Ca, Zn, Fe, Mg, Cu, and Mn; being Ca the macroelement detected at the highest concentration (3.06-3.17mg/100 mL). Neither HIPEF nor TT significantly affected mineral concentration of the beverages, except Fe, which augmented after HIPEF (300%) or TT (43%). During storage (56 days), mineral content in both bevearges remained highly stable, regardless of the treatment applied. 11 fatty acids were identified in untreated and processed FJ-WM beverages. Palmitic acid was detected at highest concentration (21.83-24.37 mg/100 g of fat). Immediately after HIPEF or TT, most fatty acids remained with no significant changes, only linoleic acid increased (20%) in HIPEF treated beverage. Fatty acid content of HIPEF treated FJ-WM beverages was kept constant along storage; only palmitic, linoleic and linolenic acids showed lower concentrations (12-20%) at day 56. Conversely, the concentration of most fatty acids in the heated beverage underwent a significant reduction (7-19%) with time, except palmitic acid, which remained constant. HIPEF can be considered as a potential alternative to conventional pasteurization to obtain stable mixed beverages with significant concentrations of health-related compounds.