Extensive data from metagenomic studies on microbial communities have provided a detailed insight into a hidden treasure of uncultured microorganisms, among which various are listed as key players in different ecological functions. Simultaneously, in the last two decades, advancements in identifying proteins from environmental samples established metaproteomics as a powerful tool and strengthened our ability to decode functional aspects. The improvement of initial 2D gel electrophoresis used for proteomic study at a larger scale is the foundation stone of metaproteomics. The development of high-throughput mass spectrometry and liquid chromatography coupled with mass spectrometry (LC-MS/MS) not only enhanced the accuracy of analysis but also revolutionized the complete workflow of metaproteomic studies. This updated workflow of community protein identification assisted in answering yet unsolved questions in medicine by studying the pathobiology of host key proteins and diagnosing key proteins causing disease or preventing it. It also assists in establishing plant-microbe interaction, microbe-microbe interaction, and acclimatization and tolerance of biotic and abiotic stress. The present chapter focuses on the methodological development in the metaproteomic studies, along with its recent above-mentioned application and upcoming trends.