Environmental and biotic stresses are increasing globally due to anthropogenic activities. Omics approach including metagenomics, metatranscriptomics and interactome network analysis provide an insight into a comprehensive understanding of the plant’s response to abiotic stress as heat-cold, drought and salinity. Understanding the structure and function of plant-associated microbial communities, their taxonomic composition, functional potential, dynamics of plant soil processes along with plant-soil interactions, is essential for strategizing sustainable agricultural strategies and advancing plant improvement tools, like CRISPR-Cas technologies. Transcriptome profiling using techniques, such as digital gene expression (DGE), RNA sequencing (RNA-seq), or SAGE (serial paired oligo-nucleic acid sequencing) have been done in crops like Angelica sinensis, Zea mays and other major cereal crops like wheat revealing information regarding the key regulators which play a positive role in controlling the abiotic stress responses. Chromatography techniques like gas chromatography-MS (GC-MS) and LC-MS/MS are widely used in metabolomics research due to their vast coverage of large metabolites in crops like mangosteen (Garcinia mangostana Linn.). In this article, we explain with examples, the network of transcriptional factors, plant immune hormones crosstalk and the signalling molecules involved in improved plant tolerance to abiotic stresses. We outline the instances where ‘omics’ research has pushed the boundaries of information about plant metabolites, plant gene expression pattern, soil and endophytic plant community composition, with a comprehensive view of recent advances in omics-driven research on plant gene expression, metabolites, and plant-soil-microbe interactions.