Nanosensors based on surface-enhanced Raman spectroscopy (SERS) have emerged as a class of promising optical tools for the ultrasensitive quantification of metal ions of environmental and biological interest. A central bottleneck in this field is the availability of suitable surface receptors able to convert the selective binding with these vibrationless analytes into measurable SERS signals. In this work, we tackle this issue by employing a hybrid substrate comprising a highly SERS-active plasmonic core and a ZIF-8 metal-organic framework (MOF) shell. The ZIF-8 shell firmly captures aromatic receptors close to the plasmonic structure regardless of their intrinsic affinity for the metallic surface and without altering their ability to coordinate metal ions. Furthermore, it imparts molecular sieving abilities enabling the direct use of the SERS sensing platform in complex media such as biological fluids. This was demonstrated by using different classes of chromogenic reagents (bathocuproine, a 2,6':2′,2″-terpyridine derivative, and Arsenazo III) which were exploited for the SERS detection of both transition and alkaline earth metal ions (i.e., divalent copper, cobalt and calcium ions). Notably, we successfully applied this approach for the detection of Cu(II) in untreated urine samples for Wilson's disease diagnosis. Overall, we believe this class of multifunctional hybrid substrates will serve as a valuable material for expanding the applicability of SERS spectroscopy in real-life environmental and biomedical metal ions analysis.