The main goal of this study was to synthesise and characterise different formulations based on alginate and alginate/chitosan microspheres containing nanoselenium (nano-Se) for controlled delivery applications. Nanosize elemental selenium was produced by using probiotic yogurt bacteria (Lactobacillus casei) in a fermentation procedure. The structural and morphological characterisation of the microspheres was performed by Fourier transform infrared (FTIR), X-ray diffraction (XRD) and scanning electron microscopy (SEM) analysis. FTIR and XRD pattern indicated that was an effective cross-linking of selenium nanoparticles within the polymeric matrix in both cases. The SEM images reveal that selenium nanoparticles are mainly exposed on the surface of alginate, in contrast to porous structure of alginate/chitosan/nano-Se, interconnected in a regular network. This architecture type has a considerable importance in the delivery process, as demonstrated by differential pulse voltammetry. Selenium release from both matrices is pH sensitive. Moreover, chitosan blended with alginate minimise the release of encapsulated selenium, in simulated gastric fluid, and prolong the duration of release in intestinal fluid. The overall effect is the enhancement of total percentage release concomitant with the longer duration of action. The authors' formulation based on alginate/chitosan is a convenient matrix to be used for selenium delivery in duodenum, caecum and colon.