In this study, graphene was synthesized on the Si(100) substrates via the use of direct microwave plasma-enhanced chemical vapor deposition (PECVD). Protective enclosures were applied to prevent excessive plasma etching of the growing graphene. The properties of synthesized graphene were investigated using Raman scattering spectroscopy and atomic force microscopy. Synthesis time, methane and hydrogen gas flow ratio, temperature, and plasma power effects were considered. The synthesized graphene exhibited n-type self-doping due to the charge transfer from Si(100). The presence of compressive stress was revealed in the synthesized graphene. It was presumed that induction of thermal stress took place during the synthesis process due to the large lattice mismatch between the growing graphene and the substrate. Importantly, it was demonstrated that continuous horizontal graphene layers can be directly grown on the Si(100) substrates if appropriate configuration of the protective enclosure is used in the microwave PECVD process.