In this work, Candida antarctica lipase A was applied to selectively remove saturated fatty acids from palm oil to prepare palm oil acylglycerol concentrate (POAC), where palmitic acid decreased from 40.0 to 28.7% and oleic acid increased from 40.0 to 50.5% after 3 h of hydrolysis. Lipozyme RMIM from Rhizomucor miehei was then used to incorporate either alpha linolenic acid (ALA) or eicosapentaenoic acid (EPA) into the resulting POAC. Optimum omega-3 incorporation was achieved when POAC to omega-3 ratio was 6 : 3, reaction temperature was 40 °C and reaction time was 18 h. Under these conditions, the ALA content in the separated ALA incorporated structured lipid (POAC-ALA) was 27.1%, and the EPA content in the EPA incorporated structured lipids (POAC-EPA) was 30.9%. The formed structured lipids had lower levels of saturated fatty acids, and significantly lower melting points, in both cases below 8 °C. The enzymatic process developed produces new structured lipids, with lower saturated fat and higher omega-3, with potential as a healthy palm oil derived lipid ingredient.