Microplastics (MPs) have become ubiquitous environmental pollutants, eliciting concerns about their negative impacts on terrestrial and agroecosystems. However, employing sustainable remediation approaches holds the potential to mitigate these negative impacts and bolster MPs tolerance in both the seeds and vegetative structures of plants. The current investigation explores the impact of arbuscular mycorrhizal fungi (AMF) and synthetic bacterial community (SynCom) as potential alleviators of MP-induced stress. Results exhibited that co-applied SynCom and AMF, resulted in the highest plant biomass, leaf area, pod per plant, and 100-seed weight under control (no MPs) and MPs stress. The combined application of SynCom and AMF enhanced colonization, association, and arbuscule abundance in the non-stressed plants (no MPs) as compared to stressed plants. The sole or co-application of SynCom and AMF enhanced the primary metabolites content and mitigated the MPs-induced reduction in soluble sugars, lipids, protein, and oil contents. Soybean inoculation stimulated the genes expression involved in lipid and protein biosynthesis, while a contradictory drift was noted for genes associated with lipid and protein degradation, underpinning the observed increment in protein and lipid content. Soybean inoculated with AMF exhibited the utmost α-amylase and β-amylase activities, demonstrating enhanced osmolyte (soluble sugar) production, mainly under MPs stress. Remarkably, sole or co-application further reinforces the positive effect of MPs stress on the osmoprotectants and antioxidant levels, for instance, phenol, flavonoid, glycine betaine contents, and glutathione-S-transferase (GST) activities. Subsequent to the stress release, a stress hormones known as abscisic acid (ABA) reduced in the seeds of inoculated soybean while gibberellin (GA), trans-zeatin riboside (ZR), and indole acetic acid (IAA) were increased. Therefore, it is concluded that the combined application of SynCom and AMF protected the soybean plants from MPs-induced oxidative damage by upregulating osmoprotectants and antioxidant levels. This study provides insights into the potential of sustainable remediation approaches in alleviating the complex impact of MPs on soybean, contributing to future strategies for environmental sustainability. Future studies could explore the optimization of SynCom and AMF formulations for different crops and environmental conditions, potentially leading to practical applications in sustainable agriculture and pollution management.