The potential of magnetically assisted strategies within the remit of cell-based therapies is increasing, creating new opportunities for biomedical platforms and in the field of tissue engineering and regenerative medicine. Among the magnetic elements approached for building magnetically responsive strategies, superparamagnetic iron oxide nanoparticles (SPIONs) represent tunable and precise tools whose properties can be modelled for detection, diagnosis, targeting and therapy purposes. The most investigated clinical role of SPIONs is as contrast imaging agents for tracking and monitoring cells and tissues. Nevertheless, magnetic detection also includes biomarker mapping, cell labelling and cell/drug targeting to monitor cell events and anticipate the disruption of homeostatic conditions and the progression of disease. Additionally, the isolation and screening techniques of cell subsets in heterogeneous populations or of proteins of interest have been explored in a magnetic sorting context. More recently, SPION-based technologies have been applied to stimulate cell differentiation and mechanotransduction processes and to transport genetic or drug cargo to study biological mechanisms and contribute to improved therapies. Magnetically based strategies significantly contribute to magnetic tissue engineering (magTE), in which magnetically responsive actuators built from magnetic labelled cells or magnetic functionalized systems can be remotely controlled and spatially manipulated upon the actuation of an external magnetic field for the delivery or target of TE solutions. SPION functionalities combined with magnetic responsiveness in multifactorial magnetically assisted platforms can revolutionize diagnosis and therapeutics, providing new diagnosis and theranostic tools, encouraging regenerative medicine approaches and having potential for more effective therapies. This review will address the contribution of SPION-based technologies as multifunctional tools in boosting magnetically assisted cell-based strategies to explore diagnostics and tracking solutions for the detection and analysis of pathologies, and to generate improved treatments and therapies, envisioning precise and customized answers for the management of numerous diseases.