The increasing frequency of mass bleaching events, driving extensive mortality of corals globally, highlights the need to develop approaches to preserve reef ecosystems into the future. One potential strategy under investigation is seeding of reefs with sexually produced corals. Ex situ aquaculture facilities provide a controlled environment where coral juveniles can undergo a protective grow-out phase, promoting their survival, growth and health. Little is known however about the possible benefits of applying probiotics during coral early-life development, when the coral microbiome is flexible and diverse. To address this, we first isolated > 900 bacteria from corals collected on the Great Barrier Reef. Probiotic candidates for in vivo screening were selected based on their taxonomic identity and activities. Initial in-vivo screening delivered individual bacterial strains to newly settled Acropora kenti and Platygyra daedalea in 6-well plates. Using 16S rRNA gene amplicon profiling, microbial restructuring was observed in most probiotic treatments and four candidates remained prevalent in the coral microbiome at least five days after the last inoculation. No significant changes in coral phenotype were observed in this short-term experiment, except for one Ruegeria candidate that induced tissue loss and mortality. This Ruegeria strain was therefore eliminated as a probiotic candidate and instead used as a putative pathogen in a subsequent challenge experiment. Four putative beneficial candidates (Endozoicomonas, Halomonas, Roseivivax and Pseudoalteromonas) were tested in two separate experiments with A. kenti held in flow-through systems to assess probiotic delivery strategies, and to determine if probiotic treatment provided a benefit to coral juveniles exposed to temperature stress or pathogen challenge. Our findings confirm the potential of probiotic treatments in aquaculture production of corals for reef restoration. However, further investigation is needed to refine these treatments and assess the feasibility of large-scale applications.