We introduce a passive micromixer with novel architecture using photopatterned porous polymer monoliths (PPM) and demonstrate an improvement in mixing efficiency by monitoring the fluorescence of an on-chip labeling reaction. UV light was used to photopattern a periodic arrangement of PPM structures directly within the channel of a plastic microfluidic chip. By optimizing the composition of the polymerization solution and irradiation time we demonstrate the ability to photopattern PPM in regularly repeating 100 µm segments at the tee-junction of the disposable device. To evaluate the efficiency of this dual functional mixer-reactor fluorescamine and lysine were introduced in separate channels upstream of the tee-junction and the intensity of laser-induced fluorescence resulting from the fluorogenic labeling reaction was monitored. The fluorescence level after the photopatterned periodic monolith configuration was 22% greater than both an equivalent 1 cm continuous segment of PPM and an open channel. Results indicate that this periodic arrangement of PPM, with regularly spaced open areas between 100 µm plugs of PPM, is directly responsible for enhancing the mixing and overall rate of chemical reaction in the system. In addition to facilitating preparation of a dual functional mixer-reactor, the ability to accurately photopattern PPM is an enabling technology for seamlessly integrating multiple monoliths into a single device. This technology will be particularly important to proteomic applications requiring preconcentration, enzymatic digestion and two-dimensional separations.