The development of gut microbiota-targeted small molecules represents a promising platform for the identification of new therapeutics based on the implication of human gut bacteria with different diseases. Bacterial trimethylamine (TMA)-lyase (CutC) is expressed in gut bacteria and catalyzes the conversion of choline to TMA. The association of elevated TMA production with various disorders has directed research efforts toward identification of CutC inhibitors. Herein, we introduce peptidomimetics as a promising toolbox for the discovery of CutC inhibitors. Our approach starts with screening a library of peptidomimetics for intestinal metabolic stability followed by in vitro CutC inhibition. Compound 5 was identified from this screening platform with IC value of 5.9 ± 0.6 μM for CutC inhibition. Unlike previously reported CutC inhibitors, compound 5 possessed universal CutC inhibitory activity in different bacterial strains. Molecular dynamics simulations suggested a plausible binding site and inhibition mechanism for compound 5. Therefore, compound 5 is a promising lead for further structural optimization in the search for CutC-targeted small molecules.