Bioaerosols could carry and spread harmful microorganisms, thus posing a continuous threat to human beings and livestock health. Early warning and management are crucial for controlling the spread of bioaerosols. Herein, we developed a split aptamer (SA)-based electrochemical nanosensor chip (denoted SAE-nChip) for rapid and sensitive detection of adenosine triphosphate (ATP) in bioaerosols. The platform features two components: split DNA aptamers for their ability to bind ATP and undergo target-induced assembly on the chip surface and ZIF-8@MXene composites for their ability to provide a high surface density of aptamer-binding sites and facilitate the electron transfer at the biointerface. The SAE-nChip was capable of detecting ATP with a detection limit of 10 pM. Furthermore, this assay allowed the detection of ATP in cultured microorganisms and collected real bioaerosols. Overall, this strategy of interfacing DNA aptamers with MXene-based composite materials represents a versatile approach for the ubiquitous detection of biochemical targets in bioaerosols.