Previous studies have shown that whole cells of several periodontal pathogenic bacteria including Porphyromonas gingivalis may degrade the clinically used regeneration membranes Biomend Extend and Bio-Gide. Fractionation of P. gingivalis cells revealed that cell membrane-associated proteases are responsible for the in vitro degradation of the collagen membranes. In the present study, the specific role of extracellular vesicles and the purified Arg-gingipain enzyme of P. gingivalis in the degradation of three differently cross-linked collagen membranes (Ossix; Bio-Gide and Biomend Extend) was examined. In addition, the inhibitory effect of antibacterial agents and antibiotics used in local periodontal therapy on the enzymatic degradation was evaluated. The data presented show that while all tested collagen membranes, are prone to lysis by oral bacterial proteases, cross-linked membranes are more resistant to proteolysis. Furthermore, therapeutical concentrations of the antibacterial and antibiotic agents chlorhexidine, cetylpyridiniumchloride, minocycline and doxycycline were found to partially inhibit the enzymatic breakdown of the membranes, while metronidazole had no such effect. These results suggest that the presence of P. gingivalis cells, extracellular vesicles and enzymes in the vicinity of regeneration membranes in the periodontium, may change their physical structure and therefore alter their biological properties. Furthermore, the use of cross-linked collagen membranes and antibacterial agents may significantly inhibit this proteolytic process.