In this brief, we present a multiscale simulation study of a fully depleted silicon-on-insulator (FDSOI) nonvolatile memory cell based on polyoxometalates (POMs) inorganic molecular clusters used as a storage media embedded in the gate dielectric of flash cells. In particular, we focus our discussion on the threshold voltage variability introduced by random discrete dopants (random dopant fluctuation) and by fluctuations in the distribution of the POM molecules in the storage media (POM fluctuation). To highlight the advantages of the FDSOI POM flash cell, we provide a comparison with an equivalent cell based on conventional (BULK) transistors. The presented simulation framework and methodology is transferrable to flash cells based on alternative molecules used as a storage media.