A roll-to-roll CVD system includes at least two rollers that transport a web through a deposition chamber during CVD processing. The deposition chamber defines a passage for the web to pass through while being transported by the at least two rollers. The deposition chamber includes a plurality of process chambers that are isolated by barriers which maintain separate process chemistry in each of the plurality of process chambers. Each of the plurality of process chambers includes a gas input port and a gas exhaust port, and a plurality of CVD gas sources. At least two of the plurality of CVD gas sources is coupled to the gas input port of each of the plurality of process chambers.