In this study, digested soybean protein (dspr) and peptides (dspe) were found to have different effects on the adhesion ability of Limosilactobacillus reuteri DSM17938 and HT-29 cells. Results found that dspr and dspe could increase L. reuteri adhesion ability by affecting their auto-aggregation and hydrophobicity during their stationary phase. The moonlighting protein may play a dominant role affected by dspe in the adhesion process of L. reuteri from stationary phase. Moreover, dspr and dspe also enhanced the adhesion ability of HT-29 cells to L. reuteri DSM17938, and they might play different role at different stages of adhesion. dspr mainly promoted the expression of adhesion-related genes before L. reuteri adhesion. dspe increased them after the adhesion of L. reuteri from log phase and dspr mainly enhanced their expression after stationary phase L. reuteri adhesion. Soybean protein and peptides may therefore be considered as a potential effective modulator of L. reuteri adhesion to intestinal tract.