European seabass and gilthead seabream hatcheries increasingly rely on proactive microbial management to optimize biosecurity and larval performance. Traditional biosecurity measures focused solely on microbial exclusion and disinfection are being complemented by selective microbial management across live food production stages. Hatching Artemia with EG SEP-Art D-FENSE reduced Vibrio loads by approximately five logarithmic units (99.999%) and total bacterial loads by three logarithmic units (99.9%). Subsequent water conditioning using Sanolife MIC-F (selected Bacillus subtilis, B. licheniformis, and B. pumilus strains) allowed beneficial bacteria to colonize culture systems and associate directly with rotifers and Artemia. Cold storage of Artemia nauplii in conditioned water resulted in approximately 1.6 × 10³ bacilli per nauplius without compromising nutritional quality. In gilthead seabream trials, microbially managed Artemia exhibited two-log reductions in total bacterial and Vibrio loads. Live food delivered beneficial Bacillus directly into larval tanks, where they persisted within wall biofilms for up to 30 days post-hatch (rotifers alone) or 56 days post-hatch (rotifers and Artemia combined). This strategy creates a controlled, resilient microbial ecosystem in larval rearing tanks.