Fluorescent proteins (FPs) are optical probes that are used to track the functions of genetically encoded target molecules in molecular and cellular biology. FPs have intrinsic photophysical properties generated by the chromophore and its surrounding amino acid sequences. The intensity of the fluorescence emission of FPs can be changed using external factors such as pH or metal ions. Additionally, the fluorescence intensity of FPs can be reduced or quenched using specific transition metal ions, suggesting that they are attractive probes for measuring metal ion levels. A spectroscopical analysis of the metal-induced fluorescence quenching of several FPs revealed that they exhibited intrinsic fluorescence quenching behavior with specific metal ions. The quenchable metal-binding site of FP has been determined using chemical modification, crystal structure, and modeling, providing insights into the molecular mechanism and FP engineering. In this review, studies on the change in the fluorescence activity of FPs mediated by metal ions are comprehensively compared and reviewed, and the requirements for the development of fluorescent protein-based metal biosensors in the future are discussed.