Abstract Background In the last few years, several outbreaks of nosocomial infections caused by multidrug-resistant pathogenic agents have been observed, and various biocides products were developed in order to control this phenomenon. We investigated the efficacy of two natural biodetergents composed of plants and kelps extracts, BATT1 and BATT2, against multidrug-resistant strains. Methods In-vitro antibacterial efficacy of BATT1 and BATT2 against nosocomial multidrug-resistant isolates was assessed using a suspension-inhibition test, with and without bovine serum albumin (BSA). The test was also carried out on glass surfaces with and without BSA. Results In vitro tests with both biocidal disinfectants at 25% concentration demonstrated an overall drop in bacterial, mould and yeast counts after 10 min of contact with or without organic substances. For Pseudomonas aeruginosa, it was necessary to use undiluted disinfectants with and without an organic substance. The same results were obtained in tests carried out on glass surfaces for all strains. Conclusions The natural products BATT1 and BATT2 behave like good biocides even in presence of organic substances. The use of both disinfectants may be beneficial for reducing hospital-acquired pathogens that are not susceptible to disinfectants. However, it has to be stressed that all these experiments were carried out in vitro and they still require validation from use in clinical practice.