A critical comparison between Elemental Mass Spectrometry (ICP-MS) and molecular fluorescence, as detection techniques for CdSe/ZnS Quantum Dots (QDs)-based immunoassays is presented here. Using a QDs-based progesterone immunoassay as "model" analytical system the features of both detection modes has been investigated. Minimal changes, compared to the previously developed fluorescent approach, were necessary to build the corresponding inhibition curve for the progesterone immunoassay using ICP-MS detection of cadmium (contained in the QDs core). Adequate agreement between results obtained using both elemental and molecular techniques for the determination of progesterone in cow milk has been obtained. Moreover, results from the comparison showed that fluorescence detection of the QDs is simpler, less time consuming and less expensive, but ICP-MS detection affords alternative and useful information unattainable using luminescence detection. First of all, ICP-MS allowed mass balances to be carried out (all along the sample preparation) providing an internal validation of the immunoassay procedure. Secondly, matrix-independent quantification as provided by ICP-MS enabled a direct determination of progesterone in raw milk without any further sample preparation (dilution) step. As a matter of fact, ICP-MS results showed that the quenching matrix effect suffered on bioconjugated QDs fluorescence emission (e.g. when the immunoassay was carried out directly in whole milk without any dilution) could be unequivocally attributed to nonspecific interactions between the matrix of the whole milk and the QDs surface. Finally, better sensitivity could be obtained with ICP-MS detection, IC(10)=0.028 ng/mL, versus 0.11 ng/mL using conventional fluorimetric detection, just by using lower reagents concentrations.