<p>Seed-associated microorganisms, including bacteria, fungi, archaea, and viruses, play diverse roles in seed physiology, influencing germination, seedling vigor, and long-term plant resilience. With increasing pressure to reduce synthetic inputs in agriculture, understanding the dynamics of seed microbiomes is critical for developing eco-friendly seed treatments. Recent advances in microbial engineering, bio-priming, and seed coating technologies have created new opportunities for harnessing beneficial microbes to improve germination and crop establishment under both optimal and stressful conditions. This review synthesizes current knowledge on the composition, transmission, and functional mechanisms of seed microbiomes of major crops. It highlights that germination outcomes are shaped by nutrient mobilization, phytohormone regulation, and stress buffering by beneficial microbes, as well as by pathogenic taxa that reduce viability through toxin secretion, decay, and competitive exclusion. Crucially, these effects are stage-specific, genotype-dependent, and mediated by microbe–microbe interactions. Furthermore, we examine the challenges in detection, strain compatibility, and large-scale application, and discuss emerging technologies such as synthetic microbial communities, nano delivery systems, and CRISPR-based strain optimization. We also explore potential biosafety concerns, such as horizontal gene transfer. This review presents a conceptual framework for integrating microbial-based solutions into seed systems, aiming to enhance agricultural sustainability in a changing climate.</p>