Erythritol and citric acid could be produced from waste cooking oil (WCO) by Yarrowia lipolytica under different medium conditions, and osmotic pressure together with pH were considered to be the critical factors in this process. High osmotic pressure (2.76 osmol/L) combined with low pH (pH 3.0) promoted the highest yield of erythritol (21.8 g/L) accompanied by low‐producing citric acid (2.5 g/L). By contrast, the highest citric acid biosynthesis (12.6 g/L) was detected under a pH of 6.0 and an osmotic pressure of 0.75 osmol/L, when only 4.0 g/L of erythritol was yielded. Moreover, lipase activities in these two media were also detected, and pH 3.0–OP 2.76 was supposed to be more beneficial to lipase activity. Biochemical pathways involved in the biosynthesis of erythritol and citric acid were subsequently investigated, and the products yielded from WCO were assumed to be correlated with the activities of transketolase, erythrose reductase, citrate synthase, and glycerol kinase. However, RT‐PCR analysis revealed that mRNA levels of these enzymes did not significantly differ, confirming that metabolic flux regulations of erythritol and citric acid mostly took place at the post‐transcriptional level.