In the recent past, microbiome manipulation has emerged as a promising approach to improve plant growth performance by exploring the deep insight of plant–microbe interactions. The exploration of a plant microbiome either present on an ectosphere or endosphere can provide a far better understanding about the potential application of plant-associated microbes for the improvement of plant growth, protection from pathogen invasion, and tolerance to environmental stresses of a diverse nature. In this context, next-generation sequencing methods, omics approaches, and synthetic biology have made significant progress in plant microbiome research and are being frequently used to explore the intriguing role of plant-associated microorganisms. Despite the successfulness of conventional approaches, the incorporation of CRISPR/Cas9, RNA interference technology, rhizosphere engineering, microbiome engineering, and other manipulation techniques appear to be a promising approach to enhancing plant performance, and tolerance against biotic and abiotic stress factors. The present review presents the significance of plant microbe interaction, vital functional aspects, collaborative action, potential constraints, and finally the latest developments in bioengineering approaches destined for microbiome modulation with an objective to improve the performance of a host plant challenged with environmental stressors.

Plants are associated with diverse microbial communities that play a crucial role in plant growth promotion and improving stability under stress conditions. Microbiome engineering involves the targeted manipulation, recruitment, and optimization of plant-associated microbial communities to enhance plant performance. However, the effectiveness of microbiome engineering can vary with plant genotype, environmental conditions, microbial composition, and the stability of introduced or selected communities. This review paper summarizes emerging strategies for plant microbiome engineering, including synthetic microbial consortia (SynComs) and host-mediated microbiome selection. SynCom approaches involve the rational assembly of selected microbial strains at the community scale, whereas host-mediated engineering uses plant–microbiome interactions and host genetic variation to enrich beneficial microbial communities. Evidence suggests that combining complementary microbial functions with host-mediated selection may improve microbiome establishment and functional consistency; however, translating these benefits into reliable field performance remains challenging because of context-dependent microbial interactions, competition with resident communities, and limited long-term persistence. Furthermore, this review also discusses omics technologies, including metagenomics, metabolomics, and transcriptomics, which facilitate the identification of functional microbial traits and plant–microbe interactions. Artificial intelligence and machine learning provide complementary tools for microbiome prediction and targeted intervention design. However, their predictive reliability depends on representative datasets, robust validation, and integration of environmental and biological variables. The review highlights that successful microbiome engineering requires a shift from microbial community assembly alone toward functionally validated, ecologically stable, and field-tested strategies. Integrating microbiome engineering with multi-omics, AI-driven prediction, and precision agriculture could support more predictable, resilient, and sustainable crop production.