In this study, we analysed the physico-chemical properties of positively charged magnetic fluids consisting of magnetic nanoparticles (MNPs) functionalised by different amino acids (AAs): glycine (Gly), lysine (Lys) and tryptophan (Trp), and the influence of AA–MNP complexes on the MRI relaxivity. We found that the AA coating affects the size of dispersed particles and isoelectric point, as well as the zeta potential of AA–MNPs differently, depending on the AA selected. Moreover, we showed that a change in hydrodynamic diameter results in a change to the relaxivity of AA–MNP complexes. On the one hand, we observed a decrease in the relaxivity values, r1 and r2, with an increase in hydrodynamic diameter (the relaxivity of r1 and r2 were comparable with commercially available contrast agents); on the other hand, we observed an increase in r2* value with an increase in hydrodynamic size. These findings provide an interesting preliminary look at the impact of AA coating on the relaxivity properties of AA–MNP complexes, with a specific application in molecular contrast imaging originating from magnetic nanoparticles and magnetic resonance techniques.