Somatic embryogenesis is an important tissue culture technique that sometimes leads to phenotypic variation via genetic and/or epigenetic changes. To understand the genomic and epigenomic impacts of somatic embryogenesis, we characterized soybean epigenomes sampled from ten different stages ranging from six weeks to thirteen years of continuously cultured embryos. We identified genome-wide increases of DNA methylation from all cultured samples, especially at CHH sites. The hypermethylation almost exclusively occurred in regions previously possessing non-CG methylation and was accompanied by increases in expression of RNA-directed DNA methylation (RdDM) machinery. We found the epigenomic changes are similar between somatic and zygotic embryogenesis. Following the initial global wave of hypermethylation, rare decay events of maintenance methylation were observed and the extent of the decay increased with time in culture. These losses in DNA methylation were accompanied by down-regulation of the RdDM machinery and transcriptome reprogramming reminiscent of late-stage seed development transcriptomes. These results reveal a process for reinforcing already silenced regions to maintain genome integrity during somatic embryogenesis over the short term, which eventually decays at certain loci over longer time scales.