Proprietary results on preparation and studies of whole-cell and lysates-based heterogeneous biocatalysts with different enzymatic activity were reviewed. A peculiar method was developed for preparing these biocatalysts by immuring (entrapping) enzymatic active components (EAC) inside silica (SiO2) xerogel and nanocarbons-in-silica composites. Properties of the multi-component composite biocatalysts such as enzymatic activity and operational stability were compared. The effect of the inclusion of nanocarbons such as nanotubes, nanofibers, and onion-like nanospheres with various texture, nanostructure and dispersion were thoroughly studied. With invertase-active biocatalysts, the direct correlation between an increase in the enzymatic activity of the nanocarbons-in-silica biocatalyst and efficiency of EAC adhesion on nanocarbons was observed. The steady-state invertase activity of the baker yeast lysates-based biocatalysts was determined to increase by a factor of 5–6 after inclusion of the multi-walled carbon nanotubes inside SiO2-xerogel. With lipase-active biocatalysts, the effect of the included nanocarbons on the biocatalytic properties depended significantly on the reaction type. In interesterification of oil-fat blends, the biocatalysts without any included nanocarbons demonstrated the maximal lipase activity. In esterification of fatty acids with aliphatic alcohols, the activity of the biocatalysts increased by a factor of 1.5–2 after inclusion of the aggregated multi-walled carbon nanotubes (CNTs) inside SiO2-xerogel. In the low-temperature synthesis of isopentyl esters of butyric (C4:0), capric (C10:0), and srearic (C18:0) fatty acids, the lipase-active composite CNTs-in-silica biocatalysts operated without loss of activity for more than thousand hours.