Lignocellulosic biomass pretreatment with ionic liquids (ILs) has been emerged as a new technology, but the effects of residual ILs on the downstream biotransformation remain largely unknown. Here, three typical ILs were tested for their effects on lipid production by the oleaginous yeast Rhodosporidium toruloides AS 2.1389. When cultures were maintained at pH 6.0 in the presence of 30mM ILs, [Emim]Cl, [Emim][DEP], or [Emim][OAc], minor inhibition effects were observed. When cultures were performed in the presence of 60mM ILs or without pH control, inhibition was largely dependent on ILs. Detailed analysis indicated that the anion of [Emim][OAc] was assimilated, leading to a rapid alkaline-pH shift and enhanced inhibition on cell growth and lipid production. Our results demonstrated that R. toruloides is a robust lipid producer tolerating ILs at low concentrations, and that care should be taken in bioprocess control and data analysis when ILs are involved.