In view of increasing antibiotic resistance, antimicrobial photodynamic therapy (aPDT) is an alternative treatment method used to eradicate the microbial community of oral biofilms that can be responsible for different oral infections. In order to investigate changes in the microbial composition after application of aPDT with visible light and water-filtered infrared A (VIS+wIRA) in combination with indocyanine green (ICG), oral microorganisms of the initial and mature biofilm were evaluated by mass spectrometry (MALDI-TOF-MS). To determine surviving microorganisms using MALDI-TOF-MS, an in situ biofilm was irradiated with VIS+wIRA for five minutes in the presence of ICG (300 and 450 µg/mL, respectively). Treatment with chlorhexidine (0.2%) served as positive control. Identified microorganisms of the initial biofilm treated with ICG showed a clear reduction in diversity. The microbial composition of the mature oral biofilm also showed changes after the implementation of aPDT, which mainly resulted in a shift in the percentage of bacterial species. The resulting destruction of the microbial balance within the oral biofilm by aPDT using VIS+wIRA and ICG can be seen as an advantageous supplementary approach in the adjunctive treatment of periodontitis and peri-implantitis.