We report the production of BC gels by Komagataeibacter sucrofermentans in synthetic (Hestrin and Schramm; HS) and natural media (raisin finishing side-stream extracts; RFSE), and their in situ modification by natural zeolite (Zt) and activated carbon (AC) nanostructures (NSs) carrying thyme oil (Th). The NS content for optimum BC yield was 0.64 g/L for both Zt-Th (2.56 and 1.47 g BC/L in HS and RFSE, respectively), and AC-Th (1.78 and 0.96 g BC/L in HS and RFSE, respectively). FTIR spectra confirmed the presence of NS and Th in the modified BCs, which, compared to the control, had reduced specific surface area (from 5.7 to 0.2-0.8 m2/g), average pore diameter (from 264 to 165-203 Å), cumulative pore volume (from 0.084 to 0.003-0.01 cm3/g), crystallinity index (CI) (from 72 to 60-70%), and crystallite size (from 78 to 72-76%). These values (except CI and CS), slightly increased after the use of the BC films as antimicrobial coatings on white cheese for 2 months at 4 °C. Tensile properties analysis showed that the addition of NSs resulted in a decrease of elasticity, tensile strength, and elongation at break values. The best results regarding an antimicrobial effect as cheese coating were obtained in the case of the RFSE/AC-Th BC.