The establishment of the early-life gut microbiota plays an important role in fish development and influences the host's health status and growth performance. Different rearing conditions can impact the initial colonization of the gut microbiota, while the addition of probiotics may also affect such colonization. However, how this may affect fish larvae survival and growth remains largely unexplored. In this study, 3-day old Nile tilapia embryos were hatched until 9 days post fertilization (dpf) in three systems, including one flow-through system (FTS) and two identical recirculating aquaculture systems (RAS). When feeding started at 10 dpf, tilapia larvae in the FTS and one of the RAS were fed with a control diet, while larvae in the second RAS were fed with the control diet coated with B. subtilis spores (RASB). The feeding trial lasted 26 days, from larvae to fry stage, during which the survival, growth performance and gut microbiota were analyzed. The larvae reared in FTS showed significantly lower survival than those in RAS and RASB, while no differences were observed in fish growth and apparent feed conversion ratio between treatments. Different rearing systems resulted in different gut microbiota compositions, which strongly correlated with the survival rate and standard body length at harvest. Cetobacterium was enriched in RAS and RASB, while was barely detected in the gut of FTS-reared tilapia fry. Probiotic supplementation increased the relative abundance of beneficial Bacillus in fish gut. Our findings indicate that rearing fish larvae in RAS supports better survival compared to FTS, while dietary probiotic supplementation further modulates the gut bacterial composition and stimulates presence of beneficial bacteria during early life.