A critical bottleneck for bivalve hatcheries is the availability of mature broodstock with high-quality gametes to ensure the production of healthy spat. The use of highly diluted bioactive compounds (HDBC) has emerged as a novel and prophylactic strategy to improve gonad development, reproduction bioenergetics, and oocyte quality of marine bivalve broodstock. This study evaluates the effect of HDBC formulas to enhance the laboratory-controlled breeding capacity of Modiolus capax adult mussel, selected as a model organism because of its aquaculture potential as an alternative seafood resource. The experimental design included three replicates of three HDBC treatments at 31Centesimal (1 × 10−31) dynamizations using distilled water as the final excipient (TR1: SiT, CaS, HeS; TR2: PhA, FeP, ZnP; and TR3: ViP, ViA, ViT), and two control treatments: C+ hydro-alcoholic solution at 1% (Usual HDBC vehicle) and C- (distilled water) during a 30-day period. As a result, TR1 enhanced energy reserves (lipids and carbohydrates) in all tissues; TR2 promoted an increase in lipid and carbohydrate content in the gonad and their transfer into developing oocytes; TR3 significantly improved gonad development and reproductive capacity of the mussels with the highest proliferation of mature oocytes, enhancing food-nutrient assimilation and energetic reserve transfer from the somatic tissues to the ovary. Additionally, all HDBC formulas recorded a lower (P < 0.05) number of atretic oocytes compared to the untreated animals. This evidence reflects a simultaneous improvement of gametogenesis and energy budget of M. capax broodstock, ensuring sexual maturation and higher-quality oocytes when HDBC are used.