The aim of the presented work was to functionalize a blend based on polyhydroxyalkanoate (PHA): poly(hydroxybutyrate (PHB) with poly(lactic acid) (PLA) and a mixture of three selected herb extracts, namely, Hypericum L., Urtica L. and Chelidonium L., (E), zinc oxide (ZnO) and a combined system (EZnO), produced via extrusion. Before processing with bioresin, the natural modifiers were characterized using thermal analysis, FTIR and antimicrobial tests. The results revealed interactions between the extracts and the filler, leading to higher thermal stability in EZnO than when using E alone. Moreover, the mixture of extracts exhibited antimicrobial properties toward both Gram-negative (S. aureus) as well as Gram-positive bacteria (E. coli). Modified regranulates were transformed into films by cast extrusion. The influence of the additives on thermal (DSC, TGA and OIT), mechanical, barrier (WVTR and OTR), morphological (FTIR) and optical properties was investigated. The EZnO additive had the highest impact on the mechanical, barrier (OTR and WVTR) and optical properties of the bioresin. The microbial test results revealed that PHA-EZnO exhibited higher activity than PHA-ZnO and PHA-E and also reduced the number of S. aureus, E. coli and C. albicans cells. The findings confirmed the synergistic effect between the additive components. Modified polyester films did not eliminate the phi6 bacteriophage particles completely, but they did decrease their number, confirming moderate antiviral effectiveness.