Denture prostheses are an ideal and extensive reservoir for microorganisms to attach to their surfaces. The aim of the study was to elucidate interactions between materials for the fabrication of denture bases and the attachment of microorganisms, focusing on respiratory pathogens and Candida species. Specimens (6 mm x 1 mm) with a standardized surface roughness (Sa = 0.1 mu m) were prepared from heat-pressed polymethyl methacrylate (PMMA), CAD/CAM-processed PMMA, and CAD/CAM-processed polyether ether ketone (PEEK). The specimens were randomly placed in the vestibular areas of complete upper dentures in seven patients and were removed either after 24 h without any oral hygiene measures or after a period of four weeks. The microorganisms adherent to the surface of the specimens were cultivated and subsequently analyzed using mass spectrometry (MALDI-TOF). The means and standard deviations were calculated, and the data were analyzed using a two-way analysis of variance (ANOVA) and Tukey post-hoc test where appropriate (alpha = 0.05). There was a significant increase (p <= 0.004) in the total bacterial counts (CFU/mL) between the first (24 h) and the second (four weeks) measurements. Regarding quantitative microbiological analyses, no significant differences between the various materials were identified. Respiratory microorganisms were detected in all samples at both measurement time points, with a large variance between different patients. Only after four weeks, Candida species were identified on all materials but not in all participants. Candida species and respiratory microorganisms accumulate on various denture base resins. While no significant differences were identified between the materials, there was a tendency towards a more pronounced accumulation of microorganisms on conventionally processed PMMA.