The development of cryo-nanoscale secondary ion mass spectrometry (CryoNanoSIMS) overcomes a key limitation of conventional NanoSIMS with the capacity to image vitrified biological material's elemental and isotopic distributions. In this study, we compare the sample processing workflows and analyses of conventional Nano-SIMS and CryoNanoSIMS applied to two biological scenarios: i) plant roots to examine the native distributions of physiologically relevant cations, and ii) host-microbe symbiosis in sea anem-ones to study metabolic interactions through stable isotope labeling. We find that the cryo-workflow ensures excellent structural preservation and allows precise subcellular mapping of diffusible ions with CryoNanoSIMS, which is essential for investigating a wide range of biological processes, including ion homeostasis, stress adaptation, and the cellular-level interaction of specific molecules (pharmaceuticals included). This technique thus opens a new frontier in the observation of biological tissue.