Cross-linked enzyme aggregates (CLEAs) of lipase from Burkholderia cepacia (BCL) were explored using different precipitants and different amount of glutaraldehyde as cross-linkers. The ‘fresh’ and ‘mature’ CLEAs-BCL was successfully encapsulated with sol-gel support. The latter showed the highest specific enzyme activity, which was 1.7 and 13.2-fold over CLEAs-BCL before encapsulation with sol-gel and free BCL, respectively. It performed high transesterification activity with the biodiesel yield of 88.5%. The ‘mature’ CLEAs-BCL presented high stability in the ranges of temperature (30-70 ºС) and pH (pH = 5-10). Scanning electron microscopy (SEM) and circular dichroism (CD) studies showed that the morph secondary structure of ‘fresh’ and ‘mature’ CLEAs-BCL was variant to some extent, which may be responsible for the catalytic activity variance.