<p>Plants live in intricate ecological niches where they are in continual contact with a wide variety of microorganisms, including both beneficial symbionts and dangerous diseases. For plants to survive and be healthy, they must be able to discriminate between these various microorganisms and deploy the proper defenses. Recent studies show that epigenetic processes, in addition to traditional signaling pathways, are essential for regulating how plants react to microbial interactions. The comprehensive summary examines how epigenetic changes control plant immunity by regulating pattern-triggered immunity (PTI), effector-triggered immunity (ETI), systemic acquired resistance (SAR), and defense priming. Additionally, we explore the role that these epigenetic variables play in the establishment and maintenance of mutualistic relationships with beneficial microbes such as plant growth-promoting rhizobacteria (PGPR), arbuscular mycorrhizal fungi (AMF), and rhizobia. The paper also highlights how chromatin-based regulatory mechanisms and non-coding RNA (ncRNA) networks, such as microRNAs, small interfering RNAs (siRNAs), and long non-coding RNAs (lncRNAs), facilitate two-way communication between microorganisms and plants. Recent developments in high-throughput sequencing and functional genomics have revealed the plasticity and memory capacity of the plant epigenome, providing intriguing opportunities for crop enhancement. Researchers are exploring the ability of epigenome editing techniques, such as synthetic transcriptional regulators and CRISPR-dCas9-based systems, to accurately modify stress-responsive genes. This review highlights the potential of epigenetic engineering as a sustainable strategy for enhancing plant immunity, stress tolerance, and symbiotic efficiency by elucidating the epigenetic frameworks that regulate interactions between microbes and plants.(Fig. 1).</p>