The aim of this work was to study the impact of the methodology of in vitro gastric digestion (i.e., in terms of motility exerted and presence of gastric emptying) and gel structure on the degree of intestinal proteolysis and lipolysis of emulsion gels stabilized by whey protein isolate. Emulsions were prepared at pH 4.0 and 7.0 using two homogenization pressures (500 and 1000 bar) and then the emulsions were gelled by heat treatment. These gels were characterized in terms of texture analysis, and then were subjected to one of the following gastric digestion methods: in vitro mechanical gastric system (IMGS) or in vitro gastric digestion in a stirred beaker (SBg). After gastric digestion, the samples were subjected to in vitro intestinal digestion in a stirred beaker (SBi). Hardness, cohesiveness, and chewiness were significantly higher in gels at pH 7.0. The degree of proteolysis was higher in samples digested by IMGS-SBi (7-21%) than SBg-SBi (3-5%), regardless of the gel's pH. For SBg-SBi, the degree of proteolysis was not affected by pH, but when operating the IMGS, higher hydrolysis values were obtained for gels at pH 7.0 (15-21%) than pH 4.0 (7-13%). Additionally, the percentage of free fatty acids (%FFA) released was reduced by 47.9% in samples digested in the IMGS-SBi. For the methodology SBg-SBi, the %FFA was not affected by the pH, but in the IMGS, higher values were obtained for gels at pH 4.0 (28-30%) than pH 7.0 (15-19%). Our findings demonstrate the importance of choosing representative methods to simulate food digestion in the human gastrointestinal tract and their subsequent impact on nutrient bioaccessibility.