Improvements to processing technologies have led to developments in product quality for the food and beverage industries. The potential of membrane filtration, specifically, was the focus of this work, as it applies to the removal of undesirable compounds from beverage products: methyl anthranilate from Concord juice, phenols from smoke-exposed grape juice, and certain minerals from acid whey.Concord grapes (Vitis vinifera × Vitis labrusca), an important crop for New York state, are widely processed into juice and jelly, but not widely used for other markets, such as premium wine production, due to the presence of methyl anthranilate (MA) and other “foxy”-smelling odorants in the juice that impairs these other market applications. Our work evaluated the use of nanofiltration followed by resin adsorption (NF-R) to remove MA from Concord juice. MA was reduced by 50% after ~40 min, and below sensory rejection threshold within 1 h, with negligible effects on color, titratable acidity, pH, and total soluble solids. We also evaluated the use of NF-R for the removal of undesirable volatile phenol (VP) glucosides in white and Concord grape juices. VP glucosides get absorbed into smoke-exposed grape berries, leading to monetary losses due to consumer rejection of resulting “ashy” flavors in the finished wine. Two model VP glucosides were added to the juice prior to NF-R processing. Exponential decreases were observed for both model VP compounds, with color reductions observed for both juices and a decrease of titratable acidity in white juice. Effects in the wine were also evaluated. The removal of calcium by precipitation was evaluated as a pre-treatment step to decrease the time needed to concentrate Greek-style yogurt (GSY) acid whey using reverse osmosis. We sought to optimize the demineralization of GSY acid whey through precipitation of Ca by addition of base (NaOH) and phosphate salts. The effects of pH (6 to 10), calcium-to-phosphorus (Ca/P) ratio (0.3 to 1.3), temperature (40 to 70 °C), and holding time (10 to 60 min) GSY whey decalcification were evaluated using response surface methodology (RSM). Ca precipitation ranged from 62-97% and was significantly affected by pH and the Ca/P ratio. Optimal conditions for Ca removal were pH ≥ 9 and a Ca/P ratio of 0.55. No improvement in RO flux was observed for GSY whey following decalcification.