The multi-epiomics fields, viz. epigenomics, epitranscriptomics, and epiproteomics, enable the detailed study of epigenetic mechanisms for controlling gene expression and phenotypic variation in plants. Epigenomics is considered as heritable changes in gene expression without the alterations in the DNA sequences. The plant epigenomics focuses on the DNA methylation and histone modifications that regulate the chromatin structure and gene accessibility. These epigenetic modifications are crucial for plant growth and development, in response to various biotic and abiotic environmental stresses, and adaptation. Likewise, epitranscriptomics delineates the RNA molecules that undergo dynamic and reversible modifications for regulating gene expression and cellular function. These RNA modifications mainly impact RNA stability, splicing, translation, and RNA–protein interactions. Simultaneously, at the intersection of epigenomics and epitranscriptomics, epiproteomics enables the detailed exploration of post-translational modifications (PTLMs or PTMs) for the modulation of protein function and cellular processes. PTLMs, viz. phosphorylation, acetylation, ubiquitination, and methylation, provide dynamic regulation to the protein activity, stability, localization, and interactions within the cell. All these approaches provide deeper understanding of complex regulatory networks governing cellular functions and pathways. Multi-epiomics with the advent of advanced next-generation sequencing approaches and computational technologies provides scrutiny in the molecular mechanisms beneath the complex traits and phenotypic plasticity leading toward crop improvement, sustainable agriculture, and stress resilience.