Indoor air quality is often measured in terms of nonviable contaminants. In the Philippines, the viable components of air have not received as much attention as the nonviable counterparts. Among the viable components of indoor air are airborne bacteria, which are potential health hazards. In this initial study, airborne bacteria present in an indoor cafeteria were characterized. Bacterial isolates from indoor air were analyzed using Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometer (MALDI-TOF MS). Mass spectral analyses of the 64 environmental isolates revealed high proportions of Staphylococcus spp., Bacillus spp., Micrococcus spp., and Lactobacillus spp. Among the Staphylococcus species identified by MALDI-TOF MS were that of S. epidermidis, S. haemolyticus, S. hominis, S. saprophyticus and S. lentus. We further investigated the metabolism profiles of Staphylococcus genus using Analytical Profiling Index (API). Notably, MALDI-TOF MS and API provided similar identification of the Staphylococcus spp. isolates. To the best of our knowledge, this is the first report of MALDI-TOF MS airborne bacterial identification in the Philippines.