Wood is a biobased material that supports long-term carbon storage; however, its suitability for use in healthcare facility interiors remains insufficiently studied. This study assessed surface microbial dynamics and residual diversity in patient rooms with conventional painted wall materials and with designer wooden wall panels. Surface microbial dynamics were evaluated using adenosine triphosphate (ATP) measurements and the swab method with colony-forming unit (CFU) counting. Bacterial and fungal cultures from each patient room were analysed by Sanger sequencing. No significant differences in ATP levels or microbial quantities were observed between rooms. In addition, no correlation was observed between ATP levels and CFU counts within each patient room due to methodological differences. In total, 37 microbial species (24 bacterial and 13 fungal) from 23 genera, all belonging to risk groups 1 and 2, were identified. Significant differences in microbial biodiversity were observed among the patient rooms studied. Fewer unique taxa were detected in the room with wooden walls. This study suggests that the installation of wooden wall panels was not associated with increased surface microbial contamination or altered microbial dynamics under the conditions investigated. The findings support the careful consideration of wood as a finishing material in hospital facilities, while highlighting the need for further replicated studies to confirm these observations.