The production of phospholipid (PL) conjugates with biologically active compounds is nowadays an extensively employed approach. This type of phospholipids conjugates could improve bioavailability of many poorly absorbed active compounds such as isomers of conjugated linoleic acid (CLA), which exhibit versatile biological effects. The studies were carried out to elaborate an efficient enzymatic method for the synthesis of phospholipids with pure (>90%) cis-9,trans-11 and trans-10,cis-12 CLA isomers. For this purpose, three commercially available immobilized lipases were examined in respect to specificity towards CLA isomers in acidolysis of egg-yolk phosphatidylcholine (PC). Different incorporation rates were observed for the individual CLA isomers. Under optimal conditions: PC/CLA molar ratio 1:6; Rhizomucor miehei lipase loading 24% wt. based on substrates; heptane; DMF, 5% (v/v); water activity (aw), 0.11; 45 °C; magnetic stirring, 300 rpm; 48 h., effective incorporation (EINC) of CLA isomers into PC reached ca. 50%. The EINC of CLA isomers was elevated for 25–30% only by adding a water mimic (DMF) and reducing aw to 0.11 comparing to the reaction system performed at aw = 0.23. The developed method of phosphatidylcholine acidolysis is the first described in the literature dealing with isometrically pure CLA and allow to obtain very high effective incorporation.