Contaminated surfaces play a major role in disease transmission to humans. The vast majority of commercial disinfectants provide short-term protection of surfaces against microbial contamination. The Covid-19 pandemic has attracted attention to the importance of long-term disinfectants as they would reduce the need for staff and save time. In this study, nanoemulsions and nanomicelles containing a combination of benzalkonium chloride (BKC; a potent disinfectant and a surfactant) and benzoyl peroxide (BPO; a stable form of peroxide that is activated upon contact with lipid/membranous material) were formulated. The prepared nanoemulsion and nanomicelle formulas were of small sizes <80 nm and high positive charge >45 mV. They showed enhanced stability and prolonged antimicrobial efficacy. The antibacterial potency was evaluated in terms of long-term disinfection on surfaces as verified by repeated bacterial inoculums. Additionally, the efficacy of killing bacteria upon contact was also investigated. A nanomicelle formula (NM-3) consisting of 0.8% BPO in acetone and 2% BKC plus 1% TX-100 in distilled water (1 : 5 volume ratio) demonstrated overall surface protection over a period of 7 weeks upon a single spray application. Furthermore, its antiviral activity was tested by the embryo chick development assay. The prepared NM-3 nanoformula spray showed strong antibacterial activities against Pseudomonas aeruginosa, Escherichia coli, and Staphylococcus aureus as well as antiviral activities against infectious bronchitis virus due to the dual effects of BKC and BPO. The prepared NM-3 spray shows great potential as an effective solution for prolonged surface protection against multiple pathogens.