Lack of replication is a recurring problem in experimental microbial ecology. Compared to natural ecosystems, replication in the laboratory is relatively easy when using batch experiments. But these results may not be relevant in an ecological context while chemostats are typically better suited for testing ecological theory. In chemostats, the dilution rate fixes the growth rate. Multiplying microbes are retained and non-growing microbes are washed out. Despite their usefulness, chemostats are rarely used in microbial ecology, and when used, often lack replication or large experimental gradients due to the complexity of the set-up and costs of operation. We developed a simple, mostly automated multiplexed system of lab-scale chemostats for testing fundamental questions in microbial ecology, e.g. community responses to disturbances, competition, or community assembly. In our research, we quantify diversity effects on ecosystem function when making different anaerobic digester communities directly compete with each other. We hypothesize that exposure to other communities enhances the generation of novel interactions between community members and may affect ecosystem functioning. A unit of our multiplexed system costs about US$6500 and hosts 6 chemostats. Several units can be run in parallel. The working volume, dilution rate and temperature can be tuned as desired. Sterile feeding, biomass wasting, quantification of biogas production and degassing are fully automated. The chemostats can be maintained under strictly anaerobic conditions over several weeks. The versatility of our multiplexed system makes the use of chemostats a feasible option for meaningful ecological experiments.