Mixed-phase thin film materials, consisting of nanocrystalline semiconductors embedded within a bulk semiconductor or insulator, have been synthesized in a dual-chamber co-deposition system. A flow-through plasma reactor is employed to generate nanocrystalline particles, that are then injected into a second, capacitively-coupled plasma deposition system in which the surrounding semiconductor or insulating material is deposited. Raman spectroscopy, X-ray diffraction and high resolution TEM confirm the presence of nanocrystals homogenously embedded throughout the a-Si:H matrix. In undoped nc-Si within a-Si:H (a/nc-Si:H), the dark conductivity increases with crystal fraction, with the largest enhancement of several orders of magnitude observed when the nanocrystalline density corresponds to a crystalline fraction of 2 – 4%. These results are consistent with the nc donating electrons to the surrounding a-Si:H matrix without a corresponding increase in dangling bond density for these films. In contrast, charge transport in n-type doped a/nc-Si:H films is consistent with multi-phonon hopping, possibly through extended nanocrystallite clusters with weak electron-phonon coupling. The flexibility of the dual-chamber co-deposition process is demonstrated by the synthesis of mixed-phase thin films comprised of two distinct chemical species, such as germanium nanocrystallites embedded in a-Si:H and Si nanocrystallites embedded within an insulating a-SiNx:H film.