The objective of this study was to develop inexpensive and facile nanocomposites based on chitosan and organo-clay with the antimicrobial affectivity that provide the serious challenges caused by bacterial infections in various products such as food packaging materials. The chitosan with octadecylamine montmorillonite (ODA-MMT) nanocomposites by supplementing 1, 2.5, and 5 w% Nigella arvensis seed (black cumin) extract (CMBC-1, CMBC-2.5, and CMBC-5) were prepared chitosan from ionic liquid solutions in the presence of ODA-MMT and black cumin extract suspension. The effect of black cumin with different content on the structure and antimicrobial activity of the nanocomposite have been investigated. The interactions between the chitosan matrix, ODA-MMT, and black cumin extract at different conditions were characterized both physicochemically (FT-IR, SEM, and XRD) and biologically (antimicrobial). The results indicated that the formation of exfoliated nanostructure of nanocomposites was provided by loading of nanodispersed clay in matrix. Antimicrobial activity of CMBC nanocomposite film was evaluated using disc diffusion method against Gram-negative bacteria Escherichia coli ATCC 25922 and Salmonella enterica serotype Typhimurium SL 1344 and Gram-positives Staphylococcus aureus ATCC 25923 and Streptococcus mutans ATCC 25175. The antimicrobial activity studies of the CMBCs illustrated that the nanocomposites could more strongly inhibit the growth of the tested Gram-negative bacteria than Gram-positive bacteria within increased content of black cumin from 1 to 5 w%. To our knowledge, this is the first report on the antimicrobial effect of CMBC nanocomposite film. Such biomaterials within nontoxic and inexpensive properties will thus have great potential applications in the development of new packing materials that can effectively prevent the antimicrobial formation.