Ocean acidification (OA) is expected to decrease the strength of bivalves’ shells, especially during the early stages of development, with negative consequences to the resilience of natural populations and the economy. The objectives of the present study were to assess the long-term effect of increasing pCO2 after 217 days of exposure under controlled conditions of pH of ∼8.2, 8.0, and 7.7 on the strength and integrity of shells of juveniles of the commercial striped venus clam Chamelea gallina. Shell strength was estimated through compression tests and integrity through scanning electron microscopy (SEM) and dispersive X-ray analyses (EDX). The results showed that under increasing pCO2 the shell strength of juveniles is unaffected, which could be related to the locally elevated total alkalinity of seawater with respect to other parts of the coastal lagoon. However, despite this, it was also observed that the juvenile clams exposed to elevated pCO2 decreased their shell thickness and increased the porosity of their prismatic layer. Under future OA conditions, these changes could eventually compromise the integrity of the shells, becoming more vulnerable to the attack of predators and breakable during fishing operations. Future studies should address the plasticity of the organisms and the effect of the alkalinization of seawater on the resilience of shellfish juveniles under global change conditions.