Cadmium (Cd) is a hazardous metal that can accumulate in aquatic organisms and endanger human health via the food chain. In this study, genetic engineering was used to display a peptide with Cd-binding potential on the surface of Escherichia coli cells. This whole-cell adsorbent exhibited high affinity for Cd ions (Cd2+) in the solution. The Cd2+ adsorption capacity of the whole-cell adsorbent was three-fold that of the control cells in a 20 μM Cd2+ solution, and 97.2% ± 2.38% of the Cd2+ was removed. The whole-cell adsorbent was fed to shrimp (Neocaridina denticulata), and the surface-engineered E. coli successfully colonized the shrimp intestine, which showed significantly less Cd accumulation than the group not fed surface-engineered E. coli. The whole-cell adsorbent evidently protected shrimp from the toxicity of Cd2+ by adsorbing it. Moreover, the whole-cell adsorbent mitigated the changes in microbial community structure in the shrimp gut caused by the exposure of Cd2+. These findings suggest that this strategy is effective for controlling the contamination of Cd2+ in shrimp. Display omitted •A cell surface display system is used to improve the adsorption of Cd2+.•The whole-cell adsorbent exhibited efficient adsorption capacity for Cd2+.•Whole-cell adsorbent in shrimp gut facilitated Cd2+ excretion.•The surface-engineered E. coli reduced Cd2+ accumulation in shrimp tissue.