Air filtration has become a desirable route for collecting airborne microbes. However, the potential biotoxicity and sterilization of current air filtration membranes often lead to undesired inactivation of captured microbes, which greatly limits microbial non-traumatic transfer and recovery. Herein, we report a gel-confined phase separation strategy to rationally fabricate a fully bio-based filtration membrane (SGFM) using soluble soybean polysaccharide and gelatin. The versatile SGFM features fascinating honeycomb micro-nano architecture and hierarchical interconnected porous structures for microbial capture, and achieves a lower pressure drop, higher interception efficiency (99.3%), and superior microbial survivability than commercial gelatin filtration membranes. Particularly, the water-dissolvable SGFM can greatly simplify the elution and extraction process after bioaerosol sampling, thereby bringing about maximum sample transfer and vigorous recovery of collected microbes. Meanwhile, green capture coupled with ATP bioluminescence endows the SGFM with rapid and quantitative detection capability for airborne microbes. This work may pave the way for designing green protocols for the detection of bioaerosols.