Bioaerosols are emitted from various sources into the indoor environment and can positively and negatively impact human health. Humans are the major source of bioaerosol emissions indoors, specifically for bacteria. However, efficient sampling to guarantee successful downstream analyses can be challenging due to the relatively low bioaerosol concentrations in many indoor spaces and variable susceptibility of bioaerosols to sampling stress. Establishing standard procedures for collecting bacteria in low biomass indoor environments can help advance the field. We compared the performance of two approaches (sampling with a personal environmental monitor (PEM) and a two-stage dry cyclone sampler) to capture the bacterial emission from human participants in a controlled chamber environment. The comparison was based on quantifying the DNA yield and characterizing the bacterial community diversity by metabarcoding of the 16S rRNA gene. We found notable differences in the performance of the samplers. The cyclone sampler collected significantly more DNA and 16S rRNA gene copies including Gram-negative bacteria than the PEM sampler (p < 0.001). The bacterial barcode sequencing revealed a significant difference in the diversity of bacteria captured by the two samplers (p < 0.05), with a higher diversity of Gram-negative bacteria captured by PEM than the cyclone sampler. Overall, this study showed that both sampling approaches efficiently sampled in low biomass indoor environments, however with substantial differences in captured DNA concentrations, bacterial concentrations, and bacterial diversity. Our results indicate that bioaerosol sampler choice is highly research question dependent, and this study provides data support to make informed choices.