Influenza A H1N1/2009 is a highly infectious, rapidly spreading airborne disease that needs to be monitored in near real time, preferably in a microfluidic format. However, such demonstration is difficult to find as H1N1 concentration in aerosol samples is extremely low, with interference from dust particles. In this work, we measured Mie scatter intensities from a microfluidic device with optical waveguide channels, where the antibody-conjugated latex beads immunoagglutinated with the target H1N1 antigens. Through careful optimizations of optical parameters, we were able to maximize the Mie scatter increase from the latex immunoagglutinations while minimizing the background scatter from the dust particles. The aerosol samples were collected from a 1:10 mock classroom using a button air sampler, where a nebulizer generated aerosols, simulating human coughing. The detection limits with real aerosol samples were 1 and 10 pg/mL, using a spectrometer or a cell phone camera as an optical detector, respectively. These are several orders of magnitudes more sensitive than the other methods. The microfluidic immunosensor readings are in concordance with the results of reverse transcription polymerase chain reaction. The assay time was 30 s for sampling and 5 min for the microfluidic assay.