Composite multi-component biocatalysts were prepared by entrapping lysates of a recombinant rE. coli/lip strain producing Thermomyces lanuginosus lipase into composite nanocarbon-containing matrices based on a SiO2 xerogel. The dependence of the lipase activity and operational stability on the type of the carbon component (nanotubes or nanospheres of different diameters) was studied in the bioconversion of triglycerides (hydrolysis and interesterification), as well as in the esterification of saturated fatty acids—namely, butyric (C4:0), capric (C10:0), and stearic (C18:0) acids—with isoamyl alcohol. It was shown that the biocatalytic properties were determined by both the texture parameters of the nanostructured carbon included and the type of enzymatic reaction performed. Biocatalysts without a nanocarbon component had the highest operational stability in the batch process of interesterification of sunflower oil with ethyl acetate; the half-life time was found to be 720 h at 40°C. Biocatalysts containing carbon nanotubes of ~21 nm in diameter were five to six times more active in the batch esterification process than biocatalysts without a nanocarbon component. Biocatalysts containing carbon nanotubes catalyzed the synthesis of esters in a binary organic solvent (hexane and diethyl ether) without a loss of activity for more than 500 h at 40°C.