Previous studies have established that whey protein manufacture unit operations influence the flavor of dried whey proteins. Additionally, manufacturers generally instantize whey protein isolate (WPI; ≥ 90% protein) by agglomeration with lecithin to increase solubility and wettability. Whey protein isolate is often subjected to additional postprocessing steps in beverage manufacturing, including acidification and heat treatment. These postprocessing treatments may further influence formation or release of flavors. The objective of the first study was to characterize the effect of 2 processing steps inherent to manufacturing of acidic protein beverages (acidification and heat treatment) on the flavor of non-instant WPI. The second study sought to determine the effect of lecithin agglomeration, a common form of instantized (INST) WPI used in beverage manufacturing, on the flavor of WPI after acidification and heat treatment. In the first experiment, commercial non-instantized (NI) WPI were rehydrated and evaluated as is (control); acidified to pH 3.2; heated to 85°C for 5 min in a benchtop high temperature, short time (HTST) pasteurizer; or acidified to 3.2 and heated to 85°C for 30s (AH-HTST). In the second experiment, INST and NI commercial WPI were subsequently evaluated as control, acidified, heated, or AH-HTST. All samples were evaluated by descriptive sensory analysis, solid-phase microextraction (SPME), and gas chromatography-mass spectrometry. Acidification of NI WPI produced higher concentrations of dimethyl disulfide (DMDS) and sensory detection of potato/brothy flavors, whereas heating increased cooked/sulfur flavors. Acidification and heating increased cardboard, potato/brothy, and malty flavors and produced higher concentrations of aldehydes, ketones, and sulfur compounds. Differences between INST and NI WPI existed before treatment; INST WPI displayed cucumber flavors not present in NI WPI. After acidification, INST WPI were distinguished by higher intensity of cucumber flavor and higher concentrations of E-2-nonenal. No perceivable differences were observed between INST and NI WPI after heating; sulfur and eggy flavors increased in both types of WPI. After treatment, AH-INST-HTST samples were differentiated from AH-NI-HTST by grassy/hay and grainy flavor and increased lipid oxidation products. Further processing of WPI in food applications has negative effects on the flavor contributions of WPI.