Marine bivalves are exposed to several environmental stressors depending on fluctuations in abiotic factors (pollutants, salinity, and temperature) and biotic factors, including ascidian biofouling. Increased seawater temperature may lead to oxidative stress in marine animals, whereas the additional burden presented by ascidian biofouling narrows their thermal window and can cause a sharper decline in shellfish health, with subsequent effects on shellfish aquaculture. The aim of the present study was to investigate the role of seawater temperature variations in the severity of the stress caused by ascidian biofouling to Mytilus galloprovincialis cell machinery, particularly in the antioxidant defense system, and the apoptotic and autophagic pathways. Fouled and nonfouled mussels were seasonally collected, and several key indicators of the previously mentioned cellular processes were determined in their mantle and posterior adductor muscle tissues. Results indicate that ascidian biofouling increases hypoxic conditions and oxidative stress, subsequently triggering cell death pathways in mussels. Although the stress caused by ascidians may be the consequence of both reduced feeding and oxygen consumption, it affects the mussels to a greater extent than seasonality. The induced stress by biofouling, along with elevated water temperatures in summer, may severely harm mussel physiology and fitness, adversely affecting aquaculture sustainability.