In this work, a microfluidic paper-based analytical device (µPAD) for simultaneous detection of Fe, Zn, and Mn ions using immobilized chromogenic reagents Ferene S, xylenol orange, and 1-(2-pyridylazo)-2-naphthol, respectively, is presented. As the effective recognition of analytes via respective chromogens takes place under extremely different pH conditions, experiments reported in this publication are focused on optimization of the µPAD architecture allowing for the elimination of potential cross effects. The paper-based microfluidic device was fabricated using low-cost and well-reproducible wax-printing technology. For optical detection of color changes, an ordinary office scanner and self-made RGB-data processing program were applied. Optimized and stable over time, µPADs allow fast, selective, and reproducible multianalyte determinations at submillimolar levels of respective heavy metal ions, which was confirmed by results of the analysis of solutions mimicking real samples of wastewater. The presented concept of simultaneous determination of different analytes that required extremely different conditions for detection can be useful for the development of other multianalyte microfluidic paper-based devices in the µPAD format.