The objective of this research was to isolate and identify lactic acid bacteria living in the digestive tract of the queen scallop Aequipecten opercularis and further test it as a probiotic culture on the growth of the bivalve during one month in captivity. Classic microbiological techniques (API and MALDI TOF) were used and four different strains of Lactiplantibacillus and one Lactococcus were identified and further analyzed, namely: Lactiplantibacillus plantarum I, Lactiplantibacillus plantarum 1, Lactiplantibacillus plantarum 2, Lactococcus lactis, and Lactiplantibacillus brevis. The isolated cultures were further tested for the highest antimicrobial activity towards the most common marine pathogens and survival at different temperatures and pH levels. The strain Lactiplantibacillus plantarum I had the best results, with the highest antimicrobial activity (77–85% pathogen growth inhibition) and the best safety standards showing no antibiotic resistance, and no ability to synthesize biogenic amine and degrade red blood cells. Considering all the abovementioned characteristics, the strain Lpb. plantarum I was further tested on the growth and health status of the bivalve Aequipecten opercularis during a month of cultivation in captivity. The results showed that the incorporation of Lpb. plantarum I led to a decrease in the quantity of test microorganisms in the bivalve and an increase in both the growth rate weight and growth rate length of the queen scallop A. opercularis. Furthermore, the scallops fed with the algae culture + Lpb. plantarum I gained significantly higher meat yield (33.15 ± 2.63%) compared with the control scallops fed only with the algae culture (29.66 ± 2.87%). To conclude, the results from this research indicate that including Lpb. plantarum I as a dietary supplement could enhance growth performance and serve as a feasible approach to reduce pathogen levels while cultivating A. opercularis in captivity.