Research has shown that increasing emulsion stability during digestion could improve nutrient encapsulation and delivery. Pectin can alter protein digestion but its effect on the digestion of protein-stabilized emulsions is not well understood. This study investigated the effect of pectin on digestion properties and encapsulation of β-carotene of whey protein-stabilized emulsion. Unheated and heated whey protein-pectin mixtures (UH-Mix and H-Mix, respectively) and biopolymer ratios were studied. H-Mix of whey protein isolate (WPI) and pectin were prepared by heating the mixed solutions (1- 5% protein and 0.1 or 0.2 pectin to protein weight ratio) at pH 7 and 85°C for 30 min. Emulsions (5% oil, 1–3% protein, and 0–0.2% pectin) were obtained by homogenizing mixed solutions with oil. Digestion was carried out in an in vitro gastric model. The mean droplet size, zeta potential, as well as β-carotene release were determined. Confocal laser scanning microscopy was used to characterize the structure of the emulsions during digestion. Results showed pectin led to a drastic increase in mean droplet sizes during digestion. At similar pectin concentration, the largest increase was from UH-Mix followed by H-Mix. Overall, droplet sizes increased when pectin increased. Zeta potential results showed no significant differences among samples. Confocal images revealed that emulsions stabilized by unheated or heated WPI had the highest degree of coalescence. Extensive flocculation but less degree of coalescence was observed in emulsions containing pectin. Emulsions stabilized by H-Mix were composed of smaller and well-defined droplets compared. Coincided with the microscopy results, H-Mix systems also had the lowest β-carotene release at the end of digestion (e.g., 6.4% release compared with 17% release in systems without pectin). Furthermore, when the emulsions contained higher protein β-carotene release decreased. We concluded that heating, biopolymer concentration, and protein concentration in the emulsions played the major roles in stabilizing the emulsion and β-carotene during digestion. Results can be applied to improve delivery properties of WPI-stabilized emulsions.