This work reports on the study of three samples of 8 nm Co-ferrite particles prepared by standard methods based on the thermal decomposition of metal–organic precursors. Although all samples are single phase according to conventional techniques of structural and chemical characterization, they show strongly sample-dependent magnetic properties ranging from bulk-like ferrimagnetism to glassy magnetic behaviour. We show that the presence of crystallite domains associated with crystallographic defects throughout the particles leads to highly-frustrated ferrimagnetic cores that are responsible for the glassy phenomenology, while only samples almost free of structural imperfections show bulk-like magnetic properties. These results suggest the key role of the crystal quality in the large variability of magnetic properties previously reported for Co-ferrite nanoparticles. Besides, achieving control of the amount of structural defects in monodisperse, stoichiometric Co-ferrite nanoparticles can be an additional nano-structuring procedure to tailor their final magnetic properties.