This study evaluated how carbon-to-nitrogen (C/N) ratio management and probiotic supplementation in biofloc systems affect resistance to Acute Hepatopancreatic Necrosis Disease (AHPND) in Litopenaeus vannamei. Post-larvae were reared for 21 days across five treatments: autotrophic bioflocs with and without probiotics (Bacillus subtilis and B. licheniformis), heterotrophic bioflocs (C/N 18) with and without probiotics, and a flow-through control. A 96 h immersion challenge with pathogenic Vibrio parahaemolyticus was conducted under three exposure scenarios: in new seawater, in respective biofloc suspensions, or using naive shrimp in biofloc suspensions. Shrimp challenged in new seawater experienced high mortality regardless of prior rearing history (1.6% to 33.3% survival). When challenged directly within biofloc suspensions, survival reached 93.3% to 100% in heterotrophic bioflocs (with and without probiotics) and 100% in autotrophic bioflocs with probiotics, compared to 46.6% in autotrophic bioflocs without probiotics and 0% in flow-through controls. Similar protective effects occurred in naive shrimp placed into bioflocs. The results demonstrate that protection against AHPND is driven by the mature microbial water suspension rather than long-term host immunomodulation.