Greek style yogurt in the United States is one of the largest growing sectors in the dairy industry. Greek yogurt is produced by removing a part of water and water-soluble components from yogurt. Consequently, a large quantity of Greek yogurt whey (GYW) is being produced as a co-product. The GYW is compositionally different from cheese whey, and thus posing economic and environmental challenges to the dairy industry. The objective of the present work was to evaluate the use of magnetic fluid treatment (MFT) and addition of sepiolite (IMV Nevada, NV), a clay mineral, as alternative methods for separating valuable GYW components. The MFT chamber was designed using 4 pairs of neodymium magnets arranged to produce a magnetic field strength of 0.6 Tesla. The GYW was pumped through the MFT chamber at a flow rate of 7.5 L/min. Three batches of GYW each from 2 manufacturers were procured. A 2 × 3 factorial design was used with MFT or no MFT and the addition of 0, 2, or 4 g of sepiolite for 100g of GYW. The pH of GYW was adjusted to 7.2 using 5 N NaOH, and processed in the MFT chamber. The sample was split into 3 sub-samples, heated to 80°C, and sepiolite was added as per the experimental design. Subsequently, the samples were centrifuged at 1000g for 5 min. The supernatant aqueous layer was separated and analyzed for total solids, ash, lactose, protein, calcium, phosphates, sodium, and color. Data were analyzed separately for each manufacture using the MIXED procedure in SAS software. MFT and its interaction did not significantly (P > 0.05) influence the analyzed whey components except for lactose. However, the addition of sepiolite significantly (P < 0.001) influenced the protein content, a*, and b* for the top aqueous layers. Both levels of sepiolite addition resulted in about a 50% decrease in protein compared with original GYW. Adding 2g of sepiolite per 100g of GYW form manufacturer 1 resulted b* decreasing from 25.99 to 8.16 compared with treated GYW with no sepiolite. Sepiolite was found to have possible applications in the removal of proteins and color pigments in Greek yogurt whey.