Fullerenes are carbon allotropes, and they have called the attention of scientists in the last 15 years. In nanotechnology, fullerenes have had several promising applications in medicinal chemistry, pharmaceutical sciences, biomedicine, and related disciplines. Particularly, the design and biological evaluation of fullerene-C60 derivatives as antimicrobial agents constitute essential components of several active areas of research that continue to grow. There is a serious concern due to the emergence of resistance of pathogens to current antibiotics, and consequently, the task of finding new and more efficient antimicrobial therapies is increasingly challenging. This review is devoted to discuss the most recent advances in the discovery of structures containing fullerene-C60as models of nanoentities-based antibacterial agents. In addition, by considering the role of the toxicity associated to the nanoparticles, we introduce a general multitasking model for quantitative-structure biological effect relationships (mtk-QSBER). This model was created from a heterogeneous dataset containing more than 47200 statistical cases, and it was focused on performing simultaneous predictions of multiple ADMET (absorption, distribution, metabolism, elimination) properties. The mtk-QSBER model could correctly classify more than 90% of the cases in the whole database, being employed for virtual screening of diverse ADMET profiles of different molecular architectures containing fullerene-C60. The theoretical results were in agreement with the experimental evidences, confirming that the increment in the number of polar regions associated to fullerene-C60 can improve the safety profiles. At the same time, this fact demonstrated the ability of the present mtk-QSBER model to be used as an efficient tool for in silico assessment of different safety profiles of large libraries of compounds under dissimilar experimental conditions.