Apparatus and method for plasma deposition of thin film photovoltaic materials at microwave frequencies. The apparatus avoids deposition on windows that couple microwave energy to deposition species. The apparatus includes a microwave applicator with one or more conduits that carry deposition species. The applicator transfers microwave energy to the deposition species to energize them to a reactive state. The conduits physically isolate deposition species that would react or otherwise combine to form a thin film material at the point of microwave power transfer and deliver the microwave-excited species to a deposition chamber. Supplemental material streams may be delivered to the deposition chamber without passing through the microwave applicator and may combine with deposition species exiting the conduits to form a thin film material. Precursors for the microwave-excited deposition species include fluorinated forms of silicon. Precursors for supplemental material streams include hydrogenated forms of silicon.