pCO2/pH perturbation experiments were carried out under two different pCO2 levels to evaluate effects of CO2-driven ocean acidification on semi-continuous cultures of the marine diatom Skeletonema pseudocostatum CSA48. Under higher pCO2/lowered pH conditions, our results showed that CO2-driven acidification had no significant impact on growth rate, chlorophyll-a, cellular abundance, gross photosynthesis, dark respiration, particulate organic carbon and particulate organic nitrogen between CO2-treatments, suggesting that S. pseudocostatum is adapted to tolerate changes of ~0.5 units of pH under high pCO2 conditions. However, dissolved organic carbon (DOC) concentration and DOC/POC ratio were significantly higher at high pCO2, indicating that a greater partitioning of organic carbon into the DOC pool was stimulated by high CO2/low pH conditions. Total fatty acids (FAs) were significantly higher under low pCO2 conditions. The composition of FAs changed from low to high pCO2, with an increase in the concentration of saturated and a reduction of monounsaturated FAs. Polyunsaturated FAs did not show significant differences between pCO2 treatments. Our results lead to the conclusion that the balance between negative or null effect on S. pseudocostatum ecophysiology upon low pH/high pCO2 conditions constitute an important factor to be considered in order to evaluate the global effect of rising atmospheric CO2 on primary productivity in coastal ocean. We found a significant decrease in total FAs, however no indications were found for a detrimental effect of ocean acidification on the nutritional quality in terms of essential fatty acids.