In this context, metaproteomics plays a crucial role in advancing microbial effector research through two key contributions: (i.): Metaproteomics aids in identifying new antimicrobial effectors by enabling the selection of microbiomes with a high abundance of proteins associated with microbial effectors. Therefore, it should be applied across various environments to maximize the number of novels identified microbial effectors. Environments under selective pressure-such as reptile saliva, amphibian skin, hospital wastewater, and livestock enclosures-are particularly interesting for discovering novel compounds. (ii.) Metaproteomics allows for the analysis of expressed proteins and phages; it is an ideal tool for examining the effects of microbial effectors.