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Probiotics gained significant attention for their potential to improve gut health and enhance productivity in animals, including poultry. This comprehensive study focused on the genetic analysis of <i>Lactiplantibacillus plantarum</i> 18 (LP18) to understand its survival and colonization characteristics in the gastrointestinal tract. LP18 was supplemented in the late-stage diet of laying hens to investigate its impact on growth performance, egg quality, and lipid metabolism. The complete genome sequence of LP18 was determined, consisting of 3,275,044 base pairs with a GC content of 44.42% and two circular plasmids. Genomic analysis revealed genes associated with adaptability, adhesion, and gastrointestinal safety. LP18 supplementation significantly improved the daily laying rate (<i>p</i> < 0.05) during the late-production phase and showed noteworthy advancements in egg quality, including egg shape index (<i>p</i> < 0.05), egg albumen height (<i>p</i> < 0.01), Haugh unit (<i>p</i> < 0.01), and eggshell strength (<i>p</i> < 0.05), with notable improvements in eggshell ultrastructure. Additionally, LP18 supplementation resulted in a significant reduction in serum lipid content, including LDL (<i>p</i> < 0.01), FFA (<i>p</i> < 0.05), and Gly (<i>p</i> < 0.05). These findings provide valuable insights into the genomic characteristics of LP18 and the genes that support its survival and colonization in the gastrointestinal tract. Importantly, this study highlights the potential of LP18 as a probiotic candidate to enhance productivity, optimize egg quality, and modulate lipid metabolism in poultry production.