Silicon oxide (SiOx) has many applications, including as a low-refractive index material. Plasma enhanced chemical vapor deposition (PECVD) processes are facile, low temperature routes to produce thin SiOx layers. A route to decrease the refractive index of SiOx films is to increase the layer porosity although maintaining structural and optical stability remains challenging. Organic carbon-containing sacrificial layers have been shown to modify the growth and resulting structure of PECVD SiOx layers. In this work, we study the effect of adding methane (CH4) to the standard SiOx process gas mixture (silane and nitrous oxide) and varying deposition temperatures and microwave power in an industrial-scale, microwave PECVD reactor. Spectral ellipsometry was used to measure the optical properties of deposited layers, Fourier-transformed infrared (FTIR) spectroscopy to determine bonding and the layer porosity, and optical emission spectroscopy to characterize the plasma. We propose two regimes characterized by whether adding CH4 increases or decreases the refractive index and porosity of deposited layers compared to SiOx layers grown under standard conditions. However, the magnitude of the effect of adding CH4 was not large and would not find industrial application. Furthermore, the deposited layers’ refractive indices increased over time, indicating that the effects of adding CH4 to the process gas mixture were not stable. To help explain our results and to provide guidance for future efforts to better control the refractive index of PECVD SiOx layers via carbon incorporation while maintaining layer stability, we propose possible growth pathways for our layers considering both plasma reactions and surface processes.