Solar cells based on epitaxial silicon layers as the absorber attract increasing attention because of the potential cost reduction. In this work, we studied the influence of the deposition rate on the structural properties of epitaxial silicon layers produced by plasma-enhanced chemical vapor deposition (epi-PECVD) using silane as a precursor and hydrogen as a carrier gas. We found that the crystalline quality of epi-PECVD layers depends on their thickness and deposition rate. Moreover, increasing the deposition rate may lead to epitaxy breakdown. In that case, we observe the formation of embedded amorphous silicon cones in the epi-PECVD layer. To explain this phenomenon, we develop a model based on the coupling of hydrogen and built-in strain. By optimizing the deposition conditions to avoid epitaxy breakdown, including substrate temperatures and plasma potential, we have been able to synthesize epi-PECVD layers up to a deposition rate of 8.3 Å/s. In such case, we found that the incorporation of hydrogen in the hydrogenated crystalline silicon can reach 4 at. % at a substrate temperature of 350 °C.