Methyl (ethyl) linoleate and soybean oil were efficiently transformed into their conjugated isomers (linoleic derivatives) by RuHCl(CO)(PPh 3) 3 or RhCl(PPh 3) 3 dissolved in ionic liquids (ILs), namely 1- n-butyl-3-methylimidazolium, N,N-methyl- n-butylpyrrolidinium and tetra- n-butylammonium cations associated with bromide (Br −), hexafluorophosphate (PF 6 −) and bis(trifluoromethylsulfonyl)imidate (NTf 2 −) anions. For example, methyl linoleate was converted to a mixture of conjugated products ( E, Z, Z, Z and E, E linoleic methyl esters) in up to 80% yield when catalyzed by RuHClCO(PPh 3) 3 in BMI·NTf 2 at 80 °C. In the case of RhCl(PPh 3) 3/SnCl 2 associated with BMI·NTf 2, complete conversion of methyl or ethyl linoleate was observed after 24 h at 60 °C, with an 85% selectivity for Z, E isomers. However, these reactions were accompanied by extensive transesterification side reactions between the methyl esters or triglycerides. The transesterification side reactions were strongly dependent on the anion of the ionic liquid. For example, extensive ethyl esters were formed in the reaction performed with RhCl(PPh 3) 3/SnCl 2 associated with ethanol in 1- n-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imidate IL (65%). Conversely, the reaction performed using the simple salt NBu 4·Br in combination with RhCl(PPh 3) 3/SnCl 2 showed the most impressive results, rendering a more active catalytic system (97% of isomerised soybean oil after 24 h at 60 °C) while preventing transesterification. The use of the Ru and Rh catalyst precursors in combination with ionophilic phosphines decreased metal leaching into the product phase.