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.