Microalgae have gained attention due to their higher reproduction rate and lipid productivity. In particular, various stress conditions lead to an overproduction of lipids in microalgae cells. The study investigated the influence of additional CO2 introduced with air into the reactor during biomass growth of Chlorella sp. Additionally, increased phosphorus concentration in the medium under stress cultivation (low nitrogen concentration) was examined. The partial pressure of CO2 and its increased availability to Chlorella sp. in the cultivation medium increased biomass growth (1.4 times) and chlorophyll content (2.5 times) in microalgae cells. A high phosphorus fertilizer significantly increased lipid production under stress conditions with CO2 supply to 85.2 mg/g (2.6 times) and without CO2 to 73.8 mg/g (2.2 times). A high concentration of phosphorus in the culture medium stimulated the synthesis of C16:0 (about 38–45%) and C18:1 CIS9 (about 24–30%). The results confirm that the fertilizers can be used as a culture medium to induce stress and stimulate lipid production. Adjusting the composition of the fertilizers and controlling the additional CO2 supply could prove beneficial to increase the content of the desired fatty acids.