Susceptibility to chronic social stressors often results in the development of mental health disorders including major depressive and anxiety disorders. In contrast, some individuals remain resilient even after repeated stress exposure. Understanding the molecular drivers behind these divergent phenotypic outcomes is crucial. However, previous studies using the chronic social defeat (CSD) stress model have been limited by the use of bulk tissues investigating single omics domains. To overcome these limitations, here, we applied the CSD mouse model to Arc-GFP mice for investigating the mechanistic divergence between susceptibility and resilience, specifically in stress recall-activated engram nuclei. By conducting an in-depth analysis of the less-known differential methylome landscape in the ventral hippocampal engrams, we noted unique phenotype-specific alterations in multiple biological processes with an overrepresentation of GTPase-related mechanisms. Interestingly, the differentially methylated regions were enriched in ETS transcription factor binding sites (TFBSs), important targets of the Ras-ETS signaling pathway. This differential methylation in the ETS TFBSs could form the basis of persisting stress effects long after stressor exposure. Furthermore, by integrating the methylome modifications with transcriptomic alterations, we resolved the GTPase-related mechanisms differentially activated in the resilient and susceptible phenotypes with alterations in endocytosis overrepresented in the susceptible phenotype. Overall, our findings implicate critical avenues for future therapeutic applications.