Anthropogenic climate change has driven many coral reef ecosystems to the brink of collapse as extreme temperature events cause widespread bleaching and mortality. Interventions that boost coral resilience are being developed to help restore reefs, and one such intervention is the manipulation of a coral’s symbiotic algae (which greatly affects their host’s physiology). New experimentally evolved symbiont strains have shown promise in increasing their host’s thermal tolerance, but how they will perform in juvenile corals when other strains are present is unclear. This study investigates the uptake and establishment of experimentally evolved Cladocopium proliferum and Durusdinium trenchii in mixed inocula and describes the effects hosting multiple symbiont strains has on the growth and survival of juvenile corals. Our results reveal that while both strains in the mixed culture inocula were taken up, most recruits were dominated by D. trenchii. Corals hosting D. trenchii over C. proliferum also displayed faster growth despite previous studies showing the opposite. We show that the costs and benefits of hosting mixed communities are highly dependent on the identities of the individual strains therein. Finally, we discuss the development of targeted symbiont communities for use in large-scale deployments of aqua-cultured coral recruits.