This work presents an original approach to develop an integrated process to improve the nutritional characteristics of natural oils, starting with the extraction from the raw material by environmentally friendly methods and following with the production of novel acylglycerols using immobilized lipases. Specifically, 2-monoacylglycerols (2-MAGs) enriched in the omega-3 stearidonic acid (SDA) were synthesized by selective ethanolysis of extracted Echium plantagineum oil using the lipase from Thermomyces lanuginosus (TLL). Different reaction conditions were investigated to minimize the undesirable acyl migration and to ensure the purity of final products. The biocatalyst produced in our laboratory by the immobilization of TLL on a hydrophobic support reached the maximum theoretical amount of 2-MAG in only 2 h at mild reaction conditions, achieving a product enriched in omega 3 SDA (up to 25%). Moreover, the produced biocatalyst exhibited higher stability than commercial lipases. The average activity after 5 cycles was 71%, allowing several reutilization cycles and developing a feasible enzymatic process. Finally, 2-MAGs was used as starting material to synthesize structured triacyclglycerols (STAGs) in solvent-free systems. The use of molecular sieves in combination with the immobilized lipase from Rhizomucor miehei (RML) showed to be an extraordinarily fast strategy to produce pure STAGs (100% in 1h), 4 times higher than the activity showed by the commercial derivative. Thus, the enzymatic processes developed in this study open a range of possibilities to synthesize omega-3 acylglycerols with improved characteristics for essential biological functions and nutritional advantages, proving the usefulness of immobilized lipases to produce novel functional lipid.