Pathogenesis of amyloid-related diseases is related to nonnative folding of proteins with the formation of insoluble deposits in the extracellular space of various tissues. Having the unique properties of small size, large surface area, biodegradability, and relative nontoxicity, magnetic nanoparticles have drawn a lot of attention in biomedical applications. Herein, we demonstrate the effect of bare and differently functionalized magnetic MnFe2O4 nanoparticles on fibrillation of human serum albumin in vitro. The process has been monitored using Thioflavin T fluorescence, Congo red binding assay, circular dichroism, fluorescence microscopy, and transmission electron microscopy. From our experimental results, amine functionalized MnFe2O4 nanoparticles are found to inhibit formation of fibrils more effectively than bare ones, while carboxylated nanoparticles do not have a significant effect on fibrillation. This study has explored the prospects of using specific magnetic nanoparticles with appropriate modification to control self-assembly of proteins and may act as a precursor in therapeutic applications.