This study presents the synthesis and characterization of alginate-based nanocomposite peelable films, reinforced by carbon nanofibers (CNFs) decorated with nanoparticles that possess remarkable antimicrobial properties. These materials are suitable for immediate decontamination applications, being designed as fluid formulations that can be applied on contaminated surfaces, and subsequently, they can rapidly form a peelable film via divalent ion crosslinking and can be easily peeled and disposed of. Silver, copper, and zinc oxide nanoparticles (NPs) were synthesized using superficial oxidized carbon nanofibers (CNF-ox) as support. To obtain the decontaminating formulations, sodium alginate (ALG) was further incorporated into the colloidal solutions containing the antimicrobial nanoparticles. The properties of the initial CNF-ox-NP-ALG solutions and the resulting peelable nanocomposite hydrogels (obtained by crosslinking with zinc acetate) were assessed by rheological measurements, and mechanical investigations, respectively. The evaluation of Minimal Inhibitory Concentration (MIC) and Minimal Bactericidal Concentration (MBC) for the synthesized nanoparticles (silver, copper, and zinc oxide) was performed. The best values for MIC and MBC were obtained for CNF-ox decorated with AgNPs for both types of bacterial strains: Gram-negative (MIC and MBC values (mg/L): E. coli—3 and 108; P. aeruginosa—3 and 54) and Gram-positive (MIC and MBC values (mg/L): S. aureus—13 and 27). The film-forming decontaminating formulations were also subjected to a microbiology assay consisting of the time-kill test, MIC and MBC estimations, and evaluation of the efficacity of peelable coatings in removing the biological agents from the contaminated surfaces. The best decontamination efficiencies against Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa varied between 97.40% and 99.95% when employing silver-decorated CNF-ox in the decontaminating formulations. These results reveal an enhanced antimicrobial activity brought about by the synergistic effect of silver and CNF-ox, coupled with an efficient incorporation of the contaminants inside the peelable films.