Background: Antibiotic use in neonatal intensive care units (NICUs) remains high. Low antibiotic prescribing has been documented among physicians trained in complementary medicine. This study sought to identify if an NICU integrating complementary medicine has low antibiotic prescribing. Methods: We conducted a retrospective analysis at the level-2 NICU of the Filderklinik, an integrative medicine hospital in Southern Germany, to compare antibiotic use locally and internationally; to compare neonates with suspected infection, managed with and without antibiotics; and to describe use and safety of complementary medicinal products. Results: Among 7778 live births, 1086 neonates were hospitalized between 2014 and 2017. Two hundred forty-six were diagnosed with suspected or confirmed infection, their median gestational age was 40.3 weeks (range 29-42), 3.25% had a birthweight <2500 g, 176 were treated with antibiotics for a median duration of 4 days, 6 had culture-proven infection (0.77 per 1000 live births), and 2.26% of live births were started on antibiotics. A total of 866 antibiotic treatment days corresponded to 111 antibiotic days per 1000 live births and 8.8 antibiotic days per 100 hospital days. Neonates managed with antibiotics more often had fever and abnormal laboratory parameters than those managed without. Complementary medicinal products comprising 71 different natural substances were used, no side effect or adverse event were described. A subanalysis using the inclusion criteria of a recent analysis of 13 networks in Europe, North America, and Australia confirmed this cohort to be among the lowest prescribing networks. Conclusions: Antibiotic use was low in this NICU in both local and international comparison, while the disease burden was in the mid-range, confirming an association between integrative medicine practice and low antibiotic prescribing in newborns. Complementary medicinal products were widely used and well tolerated. Clinical Trial Registration number: NCT04893343.