The unabated rise in anthropogenic CO₂ emissions is predicted to strongly influence the ocean's environment, increasing the mean sea-surface temperature by 4°C and causing a pH decline of 0.3 units by the year 2100. These changes are likely to affect the nutritional value of marine food sources since temperature and CO₂ can influence the fatty (FA) and amino acid (AA) composition of marine primary producers. Here, essential amino (EA) and polyunsaturated fatty (PUFA) acids are of particular importance due to their nutritional value to higher trophic levels. In order to determine the interactive effects of CO₂ and temperature on the nutritional quality of a primary producer, we analyzed the relative PUFA and EA composition of the diatom Cylindrotheca fusiformis cultured under a factorial matrix of 2 temperatures (14 and 19°C) and 3 partial pressures of CO₂ (180, 380, 750 μatm) for >250 generations. Our results show a decay of ~3% and ~6% in PUFA and EA content in algae kept at a pCO₂ of 750 μatm (high) compared to the 380 μatm (intermediate) CO₂ treatments at 14°C. Cultures kept at 19°C displayed a ~3% lower PUFA content under high compared to intermediate pCO₂, while EA did not show differences between treatments. Algae grown at a pCO₂ of 180 μatm (low) had a lower PUFA and AA content in relation to those at intermediate and high CO₂ levels at 14°C, but there were no differences in EA at 19°C for any CO₂ treatment. This study is the first to report adverse effects of warming and acidification on the EA of a primary producer, and corroborates previous observations of negative effects of these stressors on PUFA. Considering that only ~20% of essential biomolecules such as PUFA (and possibly EA) are incorporated into new biomass at the next trophic level, the potential impacts of adverse effects of ocean warming and acidification at the base of the food web may be amplified towards higher trophic levels, which rely on them as source of essential biomolecules.