Antimicrobial substances may be synthetic, semi-synthetic or derived from natural materials. They were recognized as miracle drugs if they had strong effectiveness against harmful microorganisms and were recovered suffering patients as soon as possible. However, they become multiple resistant to pathogens if they were used improperly. This multidrug resistant problem had become a major challenge for global healthcare practitioners. The major cause of this problem was the continuous spreading of drug resistant microbes by different processes. So to overcome such problems some new methods had been developed. These methodologies had replaced conventional drugs to control the multiple drug resistance. Among these technologies one of them is the green synthesis of doxycycline derived iron oxide nanoparticles (Fe3O4NPs). They were synthesized via a simple one-pot method after mixing Fe3O4 and doxycycline in NaOH aqueous solution. Ultra Violet Visible (UV-Vis) Spectroscopy and Infrared (FTIR) spectroscopy were used for characterization of Fe3O4NPs. Doxycycline and synthesized Fe3O4NPs solutions were tested against two fungal pathogens Aspergillus flavus and Aspergillus niger. The data revealed that doxycycline showed activity against Aspergillus flavus and Aspergillus niger. These activities were dose dependent when compared to doxycycline. These findings could pave the way for finding the changing behavior associated with other drugs after capping Fe3O4NPs or other metal nanoparticles and may be used against other resistant strains.