We present the first comprehensive comparison of polyurethane foam disk passive air samplers (PUF–PASs) and active high-volume air samplers (Hi-Vol) for bioaerosol monitoring in side-by-side deployments. Using qPCR, 16S rRNA gene sequencing, and multivariate analysis, we demonstrated that the PUF–PASs detected higher bacterial biomass, as evidenced by significantly elevated gene copy numbers and estimated bacterial cells per m3 of air volume, but exhibited lower diversity compared to Hi-Vol samplers. Hi-Vol samplers recovered a more taxonomically diverse community, including transient and rare taxa, during sampling periods of 1 day and 1 week. Hi-Vol detected genera not detected in long-term PUF–PAS sampling, while PUF–PAS detected species not observed in short-term Hi-Vol. PUF–PAS samples were enriched with environmental and spore-forming persistent genera. Hi-Vol samples were enriched with opportunistic and human-associated episodic spikes in a range of bacterial species. PCoA analysis confirmed a substantial divergence in bacterial community structure by sampler type and duration. Temporal analysis results showed a progressive shift in bacterial community composition with increasing sampling duration in PUF–PAS. The findings highlight the complementary benefits of both sampler types: active air sampling for capturing short-lived human-associated bioaerosols and taxonomic richness, while passive air samplers favor biomass accumulation and chronic exposure profiling, enabling exposure assessment and ecological surveillance.