Brown ring disease (BRD) in the Manila clam is characterized by the formation of a brown deposit of conchiolin on the inner surface of the shell that gives the disease its name. The development of the signs of BRD may be favored by the entry of bacteria in the extrapallial compartments via mechanical disruptions of the periostracal lamina and/or chipping of the shell margin. To test this hypothesis, we conducted an experiment simulating clam handling under aquaculture conditions and we checked for prevalence of BRD signs. Our results assess that rough handling of Ruditapes philippinarum in presence of the bacterium Vibrio tapetis significantly increase the prevalence of BRD signs. As a consequence, our results show that minimizing manipulation and transfer of clams during culture is beneficial to avoid the development of BRD signs.