The effects of the combined use of phosphonium-based ionic liquids with different alkyl chain length of cations ([P4444]+, [P444(14)]+, [P666(14)]+) and different anions ([Br]-, [Phosp]- and [NTf2]-) in the modification of silica and during immobilization by physical adsorption of Burkholderia cepacia lipase (BCL) were evaluated for the enzymatic activity and yield of immobilization of the biocatalysts. The results indicated that the increase in the length of the alkyl chain length of cations of ionic liquid (IL) ([P666(14)]Cl) caused a greater negative effect for immobilized BCL, with a reduction of 58% in relative activity. In relation to the anion type, positive effects were observed with similar tendencies for relative activity and total activity recovery yield when using ILs with more hydrophobic anions, especially for the more hydrophobic IL ([P666(14)]NTf2), with a 232% increase on relative activity.