Salinity is a major abiotic constraint that significantly limits crop productivity by inducing osmotic stress, ion toxicity, and nutrient imbalance. Conventional strategies such as breeding, chemical amendments, and transgenic approaches are often limited by high cost, long development time, and inconsistent field performance. In this context, microbial endophytes have emerged as promising eco-friendly biostimulants capable of improving plant adaptation to saline environments through coordinated physiological and molecular regulation. This review summarizes the diversity of endophytes and highlights the key mechanisms by which they enhance plant salinity tolerance. Endophytes improve ion homeostasis by modulating Na⁺/K⁺ transport systems, including Salt Overly Sensitive 1(SOS1), High-Affinity K⁺ Transporter 1(HKT1), and Na⁺/H⁺ Exchanger (NHX) antiporters, thereby restricting Na⁺ accumulation and maintaining cellular ionic balance. They help the plant cope with stress by boosting its levels of compatible solutes, such as proline and glycine betaine. At the same time, they enhance the plant’s antioxidant defence system by increasing the activity of glutathione-related enzymes and pathways, thereby reducing reactive oxygen species-induced damage. In addition, endophytes fine-tune phytohormone signalling and lower stress through ACC deaminase activity. Recent multi-omics advances (metagenomics, transcriptomics, and metabolomics) have further revealed endophyte- driven transcriptional reprogramming of stress-responsive genes and pathways. Finally, the review examines the challenges in field translation, including host specificity, formulation stability, and colonization consistency, while outlining prospects such as microbial consortia design and genome-guided strain selection for developing next-generation endophyte-based solutions for climate-resilient agriculture.