Background <p>Endophytic bacteria serve as important resources for the development of novel biocontrol agents for sustainable agriculture. This study provides a detailed characterization of a newly isolated oat endophyte, <i>Bacillus amyloliquefaciens</i> Ba. YN.J3, using an integrated analysis of phenotypic, genomic, and comparative genomic data to explore its biocontrol and plant growth-promoting (PGP) potential.</p> Results <p>The current findings indicate that Ba. YN.J3 possessed efficient PGP and biocontrol potential both in vitro and <i>in planta</i>. Additionally, Ba. YN.J3 showed broad-spectrum antifungal activity against six major phytopathogens and was found to produce multiple cell wall-degrading enzymes (CWDEs) and siderophores, significantly increasing the growth of several crop species and regulating defense enzymes in oats. The complete 4.06&#xa0;Mb genome of Ba. YN.J3 contains numerous gene clusters encoding vital secondary metabolites (e.g., surfactin, fengycin), CWDEs, and proteins associated with PGP functions and chemotaxis. The genome also harbors a robust set of genes related to abiotic stress tolerance, suggesting its potential to survive and function effectively in challenging field environments. Furthermore, comparative genomic analysis revealed 830 strain-specific genes, including two unique gene families potentially associated with chemotaxis (flagellar rod protein FlgC) and nitrogen metabolism and assimilation (regulatory protein YutI).</p> Conclusions <p>This integrated study provides genomic insights into the dual function of Ba. YN.J3 and its unique genetic determinants. The <i>flgC</i> and <i>yutI</i> gene families, in particular, offer potential genomics insights into its targeted antagonism and nutritional self-sufficiency. Hence, the current findings highlight Ba. YN.J3 as a promising candidate for the development of effective biopesticides and biofertilizers.</p>