The compost environment consists of complex organic materials that form a habitat for a rich and diverse microbial community. The fate and role of these microorganisms, when introduced into agricultural soils or potting mixes, depend on a suite of environmental factors that include biological and chemical properties of the soil and plant type and growth stage. In this review, we broadly consider the state-of-knowledge regarding compost microorganisms and their fate in plant-soil-compost systems. We explicitly consider microbial populations during the final stages of composting and in the mature product. The changes in the soil microbial community as affected by compost amendment and interactions with plant surfaces are the main focus of this chapter. We also consider important technical advances in the field of microbial ecology that have greatly improved our understanding of compost and rhizosphere microbiology. These advanced molecular biology techniques have allowed a comprehensive description of in situ microbial communities and have started to link microbial community structure with community function, even in the absence of relevant microbial isolates.