Mesoporous silica supports (aerogels) were used to immobilize Burkholderia cepacia lipase (BC) by encapsulation (EN or ENIL), physical adsorption (ADS or ADSIL) and covalent binding (CB or CBIL) into or onto the aerogel modified with protic ionic liquid (PIL). Yield immobilization (Ya) and operational stability were determined by the hydrolytic reaction of olive oil. Ya (37% to 83% by physical adsorption) and operational stability (2 to 23 batches by encapsulation) increased when the support was modified with PIL. For immobilized derivates observed by the BET method, in this case ADS and CB for ADSIL and CBIL, increased pores size was observed, possibly due to the higher amount of BC immobilized conferring Ya and operational stability. This effect was probably attributed to the entry of the enzyme into the pores of the silica aerogel structure. SEM images showed a change in the structure and properties of immobilized lipase derived with PIL. A characteristic FTIR band was obtained for the silanol groups and amides I, IV and V, demonstrating the efficiency of immobilization of BC. The most efficient biocatalysts were ADSIL with regard to yield immobilization and ENIL for operational stability.