Whey and sunflower meals are primary by-products of dairy cheese and vegetable oil production, respectively. Due to their widespread abundance, their valorisation could enable the generation of various value-added food ingredients or products. In this study, an effort was made to utilise enzymatic pectinolysis along with other pre-treatments to generate mixtures from whey and sunflower meal (SFM). The increasing presence of SFM increased the critical denaturation temperature of the mixtures and induced less protein structural changes. In addition, the presence of complex carbohydrates in SFM enhanced water and oil holding capacities. In general, pectinase and ultrasonication led to enhanced foaming of the mixtures, although the foams were relatively short-lived. SFM inclusion limited foaming and emulsification capacities of the blends. In most cases, increasing the ratio of SFM to protein resulted in lower total reducing sugars (TRS), suggesting a more limited enzymatic activity. On the other hand, heating temperature or ultrasonication improved the extent of pectinolysis. Pre-treatments and pectinolysis improved the functional properties of SFM and whey protein concentrate blends and are promising as an alternative protein source in new product applications.