<p>The present agricultural scenario with soil infertility, low productivity, climate change, environmental pollution and local economic instability challenges calls for coordinated efforts towards global sustainable development. The role of crop-friendly microbes, thus, becomes indispensable. Standard global regulations to devise and implement sustainable cropping and yield improvement measures seem emergent in such context. Microbes that are actively involved in soil physiology and crop growth could increase crop yield and reduce the dependency on agrochemicals, while promoting sustainable agriculture. To advance the sustainable development goals, it was essential to understand molecular mechanisms of microbial activities like N₂-fixation (<i>nif</i> genes), phosphate solubilisation (<i>phoD</i>, <i>appA</i> and <i>phnX</i>), phytohormone production (<i>ipdC</i> for indole-3-acetic acid synthesis), ACC (1-aminocyclopropane-1-carboxylate) deamination (<i>acdS</i>), thermotolerance (<i>hsp</i>) and reactive oxygen species (ROS) detoxification (<i>katE</i> and <i>sodA</i>) that underlie. Formulated crop-associated microbial consortia as synthetic microbial community (SynCom) could extend such benefits. In line with green (sustainable) farming, SynCom approach enhances the stability of a formulated allochthonous microbial community through the synergistic ecological interactions between the participating members and would promote crop productivity with lesser use of agrochemicals. Omics approach, either stand-alone or combined with advanced bioinformatics, is another strategy that employs non-culture techniques to identify microbial genome in an ecological niche and their functional traits. Such insights on the plant–microbe associations and the underlying molecular mechanisms could be useful in enhancing agricultural productivity and crop wellbeing on sustainable bases. This article is an attempt to dissect the recently reported literature, understand the underlying aspects in greater details, and present the current knowledge in a lucid and interlinked manner for a better and insightful understanding of the readers, with the future research directions.</p> Graphical Abstract <p>Plant–microbe interaction supports sustainability in agriculture through biofertilisation and biocontrol activity of PGPR by inducing nitrogen fixation, phosphorus solubilisation, ROS neutralisation, phytostimulation and provides protection from biotic/abiotic stress. This approach helps achieve sustainable development goals, promotes sustainable agriculture, enhances climatic resilience and supports resource efficient farming</p> <p></p>