Monitoring biomarkers and injected theranostic nanomaterials in tissues and organs plays a pivotal role in numerous medical applications ranging from cancer diagnostics to drug delivery. Scanning electrochemical microscopy has been demonstrated as a powerful tool to create highly resolved maps of the distributions of relevant biomolecules in cells and tissues without suffering from the optical interferences of conventional microscopy. We demonstrate for the first time the application of soft microelectrodes brushing in contact mode over large and thick tissues as well as organs that were immersed in an electrolyte solution. Amperometric currents were recorded based on the local flux of redox-active species locally and specifically generated by the biomarkers and nanomaterials to create maps of the biodistribution of graphene oxide nanoribbons in mouse livers, prognostic protein biomarkers in human melanoma and redox-active proteins in mouse heart.