Soybean proteins and peptides cooperated Limosilactobacillus reuteri (L. reuteri) in various ways to inhibit Escherichia coli (E. coli), but their impact on adhesion to intestinal cells remains unclear. This study investigated the adhesion properties of L. reuteri LR08 and E. coli JCM1649 regulated by soybean proteins and peptides. Digested soybean proteins (dpro) significantly enhanced L. reuteri adhesion and increased surface hydrophobicity more effectively than digested peptides (dpep) during early logarithmic growth. Dpro also improved L. reuteri biofilm formation and auto-aggregation in the stationary phase. Conversely, dpep markedly reduced E. coli adhesion to HT-29 cells, diminishing its biofilm formation and surface properties. The inhibitory effect of dpro on E. coli adhesion was weaker than that of dpep. These results highlight the diverse modulation of L. reuteri and E. coli adhesion by dpep and dpro, providing a theoretical basis for the use of probiotics to alleviate foodborne intestinal infections.