An epigenome is a collective name for the biochemical alterations to nuclear DNA, changes in noncoding RNA biogenesis and histone protein modification. Without altering the underlying nucleotide sequence, these modifications frequently cause gene expression variations. The variations in chromatin structure brought on by the modifications could also alter how the genome functions or behaves. Epigenomic mechanisms regulate gene expression patterns and are influenced by various environmental factors, including nutrient availability. Nutrient use efficiency (NtUE) is the ability of an organism to acquire, assimilate, and utilize nutrients effectively, with nitrogen being one of the most essential components for the growth of plants. Efficient nitrogen uptake is crucial for optimizing crop yield, reducing fertilizer usage, and minimizing environmental impact caused by nitrogen depletion. Both endogenous and external stimuli can create epigenomic alterations and phenotypic plasticity in plants. Plant epigenomics has undergone a revolution owing to the advancement of techniques, such as next-generation sequencing methods. The initial studies concentrated on genes and DNA methylation at cell level. However, with the advent of technology, the focus is shifting towards mapping the entire epigenome of an organism. Apart from their functions in RNA degradation and translational repression, small RNAs are potent in altering chromatin and target gene expression through RNA interference (RNAi). Some epigenetic modifications are heritable and can thus determine evolutionary adaptation for stress resilience. Understanding the responsible epigenetic machinery that maybe used to improve resource use efficiency to address nutritional/food security challenges is imperative.