In light of the COVID-19 pandemic, airborne bioaerosol like bacteria and viruses are a major concern for human health. Therefore, monitoring of the concentrations of these bioaerosols plays a vital role in understanding disease transmission.  Rapid, automated, quantitative and specific bioaerosol monitoring would allow for continuous assessment of airborne virus and bacteria at hospitals and similar locations. In this proof-of-concept study, we develop and characterise a continuous pathogenic bioaerosol sampler and detector. The set-up consists of three main parts. In a first step (Collection phase), the bioaerosol is sampled continuously via a particle into liquid sampler. This bioaerosol liquid flow is mixed with an immunoassay (Selection phase) and then quantified in a flow cytometer (Detection phase).  We have already successfully connected all three phases into one continuous, automated, and autonomous prototype for pathogenic bioaerosol monitoring. With a time resolution of 60 minutes (of which 15 are spent on sample acquisition) our instrument collects 99.5% of nebulized E. coli bacteria continuously. Flow cytometry results were confirmed with agar plate analyses. Plating can only account for colony forming units, while flow cytometry can count all labelled cells.  While other instruments for automated pathogen detection exist, these techniques lack either specificity, quantification, automation or time-resolution. This novel mix of methods attempts to combine all factors mentioned. Our next step is to optimize further and apply this method to airborne virus.