One promising way to reduce anthropogenic pollution of natural environments is to replace persistent chemicals with alternatives that are biodegraded at the point-of-entry. Motivated by the negative effects caused by the presence of antibiotics in municipal and industrial wastewater (e.g., the increasing emergence and spread of antibiotic resistance), we pursued such a benign-by-design framework for antibiotics. We focused on peptide-based antibiotics because of their potential to be rapidly hydrolyzed and inactivated by extracellular wastewater peptidases, which we expect to limit the emergence and spread of antibiotic resistance in wastewater and wastewater-receiving environments. The major impediment for the assessment and the (re-)design of more sustainable peptide-based antibiotics is our limited understanding of the specificity of wastewater peptidases. To address this knowledge gap, we used a set of peptides to assess the specificity of extracellular wastewater peptidases. Our results suggest that peptidase-catalyzed hydrolysis occurs at specific bonds and that there is substantial overlap in specificity across enzyme pools derived from independent wastewater treatment plants. Complementary to assessing the specificity of extracellular wastewater peptidases, we assessed the stability of the set of peptides in human blood plasma, which mimics the system in which peptide-based antibiotics used for the treatment of systemic infections need to be stable. By comparing the results from wastewater and blood plasma experiments, we identified amino-acid motifs that are hydrolyzed by extracellular wastewater peptidases but not by peptidases in human blood plasma. These motifs might be promising candidates for the (re-)design of peptide-based antibiotics. This contribution offers a significant step towards a better understanding of the fate of peptide-based antibiotics and the presented framework will create opportunities for the design of biodegradable chemicals in general.