Concerns exist regarding the negative environmental impact and health risks associated with ocean fishing and aquaculture, such as stock depletion, pollution, biodiversity loss, and toxin presence. To address these concerns, plant-based seafood analogs are being developed. Our previous study successfully created plant-based scallop analogs using pea proteins and citrus pectin, resembling real scallops in appearance and texture. This study focuses on comparing the digestive fate of these analogs to real scallops, as it can impact their nutritional properties. Using an in vitro digestion model (INFOGEST), we simulated oral, gastric, and small intestinal conditions. The analysis revealed differences in the microstructure, physicochemical properties, and protein digestibility between the plant-based scallops and real scallops. The particle size and charge followed the following similar trends for both types of scallops: the particle size decreased from the mouth to the stomach to the small intestine; the particles were negative in the mouth, positive in the stomach, and negative in the small intestine. The protein digestibility of the plant-based scallops was considerably lower than that of real scallops. For instance, around 18.8% and 61.4% of protein was digested in the stomach and small intestine phases for the real scallop (80.2% total digestion), whereas around 8.7% and 47.7% of the protein was digested for the plant-based scallop (56.4% total digestion). The lower digestibility of the plant-based scallops may have been due to differences in the protein structure, the presence of dietary fibers (pectin), or antinutritional factors in the plant proteins. These findings are crucial for developing more sustainable next-generation plant-based seafood analogs.