The inconsistent quality of compost across production cycles is often attributed to a lack of precise information on the complexity and heterogeneity of microecological systems and processes. Bulk measurements (physical, chemical and microbial) used to characterize compost further limit our ability to predict the efficacy of compost products since they obscure crucial information about variability or changes that occur at a deeper scale level. Advances in nanotechnology offer the opportunity to monitor, measure and manipulate microbial ecological systems and processes beyond the micro level. Exploring this opportunity will result in a more precise understanding of compost microbiology and strengthen predictive models for the efficacy of compost products. The aim of this review is to examine and highlight the prospective applications of nanotechnology to research work on compost microbiology. The focus is on the application of nanostructures (nanoparticles, nanodevices and nanosystems) to monitor and optimize composting processes, detect potential human and environmental health risks and enhance the effectiveness of compost products. To this end, the need for more studies using nanotechnology in compost research and application is recognized, within an economical framework that will better inform commercialization and on-farm adoption of the technology.