Multimaterial 3D printing provides a unique capability for the creation of highly complex integrated devices where complementary functionality is realized using differences in material properties. Using a single and automated print process, microfluidic devices were fabricated containing (i) an optically transparent structure for fluorescence detection, (ii) electrodes for electrokinetic transport, (iii) a primary membrane to remove particulates and macromolecules including proteins, and (iv) a secondary membrane to concentrate small molecule targets. The device was used for the simultaneous extraction and concentration of small molecule pharmaceuticals from urine, which was followed by an on-chip electrophoretic separation of the concentrated targets for quantitative analysis. Owing to the high level of functional integration inside the device, manual handling was minimal and restricted to the introduction of the sample and buffer solutions. The 3D printed sample-in/answer-out device allowed the direct quantification of ampicillin - a small molecule pharmaceutical - in untreated urine within 3 min, down to 2 ppm. These results demonstrate the potential of 3D printing for on-demand fabrication of disposable, functionally integrated devices for low-cost point-of-collection (POC) diagnostics.