This study evaluated the effects of a multi-species probiotic mixture on the growth, welfare, and survival of gilthead sea bream (Sparus aurata) during larviculture. A blend of three spore-forming strains (Bacillus subtilis, Bacillus licheniformis, and Bacillus pumilus) was administered either via bioencapsulated live prey (rotifers and Artemia) and direct water addition (Group 1) or exclusively through live prey (Group 2), compared against an untreated control. While survival rates remained similar across groups, probiotic supplementation significantly enhanced standard length and body weight at both larval (day 47 post-hatch) and juvenile stages (day 75 post-hatch). Group 2 achieved the highest performance, reaching 25.9 mm total length and 496.6 mg body weight at day 75, compared to 22.3 mm and 272.6 mg in controls. Molecular analyses confirmed these findings, showing upregulation of Insulin-like Growth Factor I (IGFI) and downregulation of Myostatin (MSTN). Furthermore, treated fish exhibited lower gene expression of 70 kDa Heat Shock Protein (HSP70) and Glucocorticoid Receptor (GR), demonstrating reduced cellular and physiological stress. Bioencapsulation in Artemia also significantly decreased presumptive Vibrio counts.