Metatranscriptomics is a powerful technique for understanding plant–microbe interactions and their roles in crop improvement and stress tolerance. The use of metatranscriptomics in agriculture will be discussed in this chapter, with particular attention paid to its ability to interpret patterns of gene expression in plants and related microbial communities under biotic (such as pathogens and pests) and abiotic (such as drought, salinity, and heat) stresses. Metatranscriptomics offers insights into nutrition mobilization, phytohormone control, and stress-responsive pathways by utilizing high-throughput RNA sequencing and sophisticated bioinformatics pipelines. Through advantageous interactions with plants, the chapter emphasizes the importance of microbial communities, such as rhizosphere and phyllosphere microbiomes, in reducing stress. Developing synthetic microbial consortia (SynComs) to improve crop resilience, host–microbe interaction, and identifying stress-responsive genes are important subjects. Furthermore, the combination of metatranscriptomic data with CRISPR/Cas9 gene editing, synthetic biology, and breeding techniques is explored as a means for producing crops that can withstand stress. Successful applications, like improving disease resistance and drought tolerance, are illustrated by case studies. Despite its potential, microbiome engineering still faces ethical issues and technological constraints. The necessity of multi-omics integration and further study to utilize metatranscriptomics for sustainable agriculture is emphasized in the chapter.