Coral reefs are among the most biodiverse ecosystems in the world, being essential for marine life. The engineers of these ecosystems, reef-building corals, live in association with a great diversity of microorganisms, which can affect their host’s health in beneficial or detrimental manners. Corals are currently threatened by climate change and other environmental stressors, that lead to the phenomenon of coral bleaching, in which these animals lose their endosymbiotic algae. Even though the stressors that cause coral bleaching are known, the exact cellular and molecular mechanisms that provoke this process are still undiscovered. The lack of information regarding micro-scale processes that happen in unhealthy corals could be resolved with more efforts in developing micro-scale studying models. The use of individual polyps that bail-out of the coral skeleton induced by acute stress has been suggested as a model to study these processes. However, little is known about how these polyps change after bailing-out of a colony, which could become a problem once reliable models should be consistent and well understood. Thus, investigating these changes and optimizing a methodology to minimize them is crucial to establish these polyps as models to study corals. Herein, we investigated microbiological changes of isolated polyps by performing an experiment to study shifts in their microbiome after the separation from the colony. Before the experiment, different methods to isolate polyps were tested to find the one that granted the highest survival. After finding that salinity-induced separation was the most efficient, this method was used to study the microbiome of coral polyps. We found that while no significant changes in the microbiome could be observed immediately after the separation of polyps from their colony compared to coral fragments, this pattern changed after two weeks. We propose that the maintenance of polyps without fixation to a substrate might be the cause for such changes, and that polyps able to attach to a substrate and regrow as a colony might still recover a microbiome composition closer to coral fragments. Finally, a new microfluidic device for fixation and maintenance of coral polyps was developed and tested for use in future experiments.