Gastric protein digestion can be influenced by food micro- and macrostructure. Understanding the interplay between microstructure and macrostructural breakdown during oral processing is crucial to enhance the nutritional value of protein-rich foods. This study compared the in vitro gastric protein digestion of whey protein gels differing in microstructure before and after mastication. Whey protein isolate was mixed with κ-carrageenan to obtain heat-induced gels differing in microstructure (homogeneous, coarse stranded, protein continuous, bi-continuous). Gel boli were collected from 14 participants. The number, size and total surface area of bolus fragments were determined. In vitro gastric protein digestion was quantified following the INFOGEST 2.0 protocol with minor modifications. Before mastication, coarse stranded gels showed the highest digestion rate (1.07 mmol L−1∙g dry matter−1/h), while homogeneous, protein continuous and bi-continuous gels showed lower and similar digestion rates (0.82–0.87 mmol L−1∙g dry matter−1/h). After mastication, the total surface area of coarse stranded gels increased 7.9-fold leading to a 1.9-fold increase in digestion rate. In contrast, a 3.4-fold increase in total surface area of bi-continuous gels caused a 2.8-fold increase in digestion rate. The total surface area of homogeneous and protein continuous gels increased 3.1- to 3.6-fold upon mastication resulting in a 1.7- to 1.9-fold increase in digestion rate. The increase in protein hydrolysis did not correlate with the degree of structural breakdown after mastication across gels differing in microstructure. We conclude that the impact of microstructure of whey protein gels on in vitro gastric protein digestion is sustained after oral structural breakdown by mastication.