A hollow cathode arc discharge is used for the roll‐to‐roll deposition of silicon‐containing plasma polymer thin films on a polymer substrate. It is found that the fragmentation of the used monomer hexamethyldisiloxane (HMDSO) increases with increasing plasma power. The higher fragmentation was related to a reduced hydrogen content as a result of breaking CH bonds. This allowed for a higher degree of cross‐linking. The latter has a positive effect on the barrier performance of the coatings. A hollow cathode arc discharge with separate anode allowed the deposition of a plasma polymer with a water vapor transmission rate (WVTR) of 0.16 g m−2 day−1 (measured at 38 °C and 90% r.h.) on a PET substrate while maintaining a deposition rate of approximately 450 nm m min−1.