Magnetic nanoparticles (MNPs) have been extensively researched and implemented in biomedicine for more than half a century due to their non-invasive nature, ease of temporal and spatial manipulation, and considerable biocompatibility. However, the complex magnetic behaviour of MNPs is influenced by several parameters (e.g., particle size, shape, composition, core-shell structure, etc.), among which the amount of transition metal doping plays an important factor. For this reason, the doping of ferrite with transition metals has been used as an effective strategy to precisely tailor MNPs to achieve satisfactory performance in biomedical applications. In this review, we first introduced the main properties of coordinated MNPs (including magnetic moment and saturated magnetisation) and provide a comprehensive overview of the mechanistic studies related to the doping of transition metal ions into ferrite to precisely modulate its magnetic properties. We also highlighted the potential mechanisms and recent advances in transition metal ion-doped MNPs (TMNPs) for bioimaging (magnetic resonance imaging and magnetic particle imaging) and tumour therapy (e.g., magneto-mechanical killing, magnetothermal therapy, and drug delivery). Finally, we summarised the current challenges and future trends of TMNPs in the biomedical field based on the latest advances by researchers.