Pathogenic bacteria are known to be one of the main factors affecting Pecten maximus larval survival in hatcheries. As a result, juvenile production often relies on the use of antibiotics during larval culture. However, limitations of the usage of chemicals such as chloramphenicol in aquaculture have been reinforced due to their negative environmental impact and alternatives are accordingly needed. Thus, the importance of bacterial transfer from oocytes to larvae has been studied here as well as procedures to limit larval mortality in P. maximus. In order to reduce bacterial contamination during larval development, we focused on two periods, broodstock conditioning and post-fertilization. The animals were conditioned for 2 months with two erythromycin treatments of 6 days, with (SA) or without sandy-bottom (NSA). The absence of sediment strongly reduced contamination by Vibrios of oocytes (NSA: 0.003 ± 0.002 CFU oocyte- 1SA: 0.57 ± 0.17 CFU oocyte- 1) and D-larvae (NSA: 0.14 ± 0.05 CFU oocyte- 1SA: 0.51 ± 0.002 CFU oocyte- 1). It also enhanced survival by 52% at 15 days post fertilization, whereas a two days antibiotic treatment of D-larvae did not improve subsequent survival, regardless of broodstock conditioning method. Furthermore, both treatments led to similar fatty acids profiles of oocytes and resulting larvae, suggesting that broodstock conditioning was physiologically similar with or without sediment. This work has shown that gametes contamination could be reduced when sandy-bottom was removed during broodstock conditioning under bacterial control with erythromycin. The present results contribute to a reduced utilization of antimicrobial agents for great scallop larval rearing in controlled condition.