Pomegranate (Punica granatum) bioactive compounds (polyphenols and anthocyanins) of juice (PJ) and ethanolic extracts (PE) were encapsulated with maltodextrin (MD) or soybean protein isolates (SPI) by spray drying using a 22 statistical factorial design for each systems studied (PJ–MD, PJ–SPI, PE–MD and PE–SPI) considering the proportion of coating material and the inlet temperature as independent variables. The stability of the bioactive compounds microcapsules powders obtained under optimal conditions for each system was studied at 60 °C in oven for 56 days. The polyphenols encapsulating efficiency was significantly better in SPI matrix whereas for anthocyanins was in MD matrix. By the other hand, during the storage, the MD microcapsules provided a significant greater protective effect on the polyphenols and anthocyanins than SPI, as was shown by the lower degradation rate constants. When the microcapsules were added to yogurt the stability of the bioactive compounds followed a similar behaviour to those without encapsulation, except for PE–MD.