An agronomic itinerary for Se biofortification of two rice cultivars (Ariete and Ceres) through foliar fertilization with sodium selenate and sodium selenite with different concentrations (25, 50, 75 and 100 g Se.ha−1), was implemented in experimental fields. The selenium toxicity threshold was not exceeded, as shown by the eco-physiological data obtained through leaf gas exchanges. The highest Se enrichment in paddy grains was obtained with selenite for both cultivars, especially at the highest doses, i.e., 75 and 100 g Se.ha−1, with approximately a 5.0-fold increase compared with control values. In paddy grains, Zn was the most affected element by the treatments with Se with decreases up to 54%. When comparing the losses between rough and polished grains regardless of the cultivars, Se species and concentrations, it was observed that only Cu, Mg and Zn exhibited losses <50%. The remaining elements generally had losses >70%. The loss of Se is more pronounced in Ceres cultivar than in Ariete but rarely exceeds 50%. The analysis by µ-EDXRF showed that, in Ariete cultivar, Se is mostly homogeneously distributed in the grain regardless of any treatments, while in Ceres cultivar, the Se distribution seems to favor accumulation in the periphery, perhaps in the bran.