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Marine sponges are known for their complex and stable microbiomes. However, the lack of a gnotobiotic sponge‐model and experimental methods to manipulate both the host and the microbial symbionts currently limit our mechanistic understanding of sponge‐microbial symbioses. We have used the North Atlantic sponge species Halichondria panicea to evaluate the use of antibiotics to generate gnotobiotic sponges. We further asked whether the microbiome can be reestablished via recolonization with the natural microbiome. Experiments were performed in marine gnotobiotic facilities equipped with a custom‐made, sterile, flow‐through aquarium system. Bacterial abundance dynamics were monitored qualitatively and quantitatively by 16 S rRNA gene amplicon sequencing and qPCR, respectively. Antibiotics induced dysbiosis by favouring an increase of opportunistic, antibiotic‐resistant bacteria, resulting in …