Fluorescence lifetime imaging microscopy (FLIM) is a powerful microscopy technique that can probe changes in metabolic state in vitro and in vivo in real-time, and can serve as diagnostic tools of pathological tissues in situ. The time-dimensional characteristic of FLIM combined with multiphoton (MP) microscopy enables the visualization of endogenous nicotinamide adenine dinucleotide (NADH) and flavin adenine dinucleotide (FAD), and the discrimination between free and protein-bound forms based on their respective lifetimes. In our work, we demonstrated how (pre-) hypoxic β-cell-composed pseudo-islets can be discriminated from healthy functional pseudo-islets based on their FLIM-based metabolic profiles. The use of FLIM during the pre-transplantation pancreatic islet selection process has the potential to improve the outcome of β-cell islet transplantation.