Despite iron-based nanoparticles gaining huge attraction in various field of sciences and technology, their application rises ecological concerns due to lack of studies on their interaction with microbial cells populations and communities, such as biofilms. In this study, Chlorella vulgaris cells were employed as a model of aquatic microalgae to investigate the impacts of L-lysine-coated iron oxide nanoparticles (lys@IONPs) on microalgal growth and biofilm formation. In this regard, C. vulgaris cells were exposed to different concentrations of lys@IONPs and the growth of cells was evaluated by OD600 and biofilm formation was analyzed using crystal violet staining throughout 12 days. It was revealed that low concentration of nanoparticles (< 400 µg/mL) can promote cell growth and biofilm formation. However, higher concentrations have an adverse effect on microalgal communities. It is interesting that microalgal growth and biofilm are concentration- and exposure time-dependent to lys@IONPs. Over long period (~ 12 days) exposure to high concentrations of nanoparticles, cells can adapt with the condition, so growth was raised and biofilm started to develop. Results of the present study could be considered in ecological issues and also bioprocesses using microalgal cells.