Selective and sensitive detection of volatile organic compounds (VOCs) is of great importance in applications involving monitoring of hazardous chemicals or non-invasive diagnosis. Here, polymethyl methacrylate nanoparticles with acetone recognition sites are synthesized and integrated into a 3D-printed microfluidic platform to enhance the selectivity of the device. The proposed microfluidic-based olfaction system includes two parylene C-coated microchannels, with or without polymer nanoparticles. The two channels are exposed to 200, 400, 800, 2000, and 4000 ppm of VOCs (methanol, ethanol, acetone, acetonitrile, butanone, and toluene), and sensor responses are compared using a 2D feature extraction method. Compared to current microfluidic-based olfaction systems, responses observed between coated and uncoated channels showed an increased recognition capability among VOCs (especially with respect to acetone), indicating the potential of this approach to increase and fine-tune the selectivity of microfluidic gas sensors.