A term newborn, who underwent lotus birth, developed Staphylococcus lugdunensis sepsis and endocarditis on the 1st day of life. This case reports an uncommon pathogen known to cause destructive endocarditis in the adult and paediatric populations, causing endocarditis in a neonate. We speculate that lotus birth, an atypical birthing practice, may have contributed to the development of this infection.