Microbial ecosystems play a major role in biogeochemical cycles, plant development and animal health. How microorganisms interact with each other, with their hosts, and with their environment are key questions. Understanding the functioning of microbial communities requires identifying the diversity of microorganisms present and quantifying the numerous molecular players in action. Proteins are the workhorses of biological systems. Metaproteomics is a key technology for such functional studies as it can provide for these particularly complex samples four types of answers: 1) identification of the taxa present, 2) quantification of the biomass of these organisms, 3) identification of the proteins of these taxa and their function, and 4) overall functional representation of the biological system. Challenges in terms of mass spectrometry, interpretation and mining of results will be addressed.