In this study, we used 16S rRNA gene sequencing approaches to characterize the bacterial microbiota on different surfaces of the hospital environment. The longitudinal data was then subjected to comprehensive comparisons between different sanitation strategies (disinfectants, detergents and probiotics) to measure their potential effect on the microbial community structures in the hospital environment. This archive contains results and data of the 16S rRNA amplicon sequencing performed on 1019 environmental and 271 patient DNA samples collected over the time course of 40 weeks in a newly opened ward in the neurological station at the Charit�� Hospital (Berlin). The files include a study information and sample metadata sheets, BIOM-tables and information about the taxonomy results and diversity metrics.