The deposition of chemical reagent inks on paper is a crucial step in the development and fabrication of microfluidic paper-based analytical devices (μPADs). A pen-plotting approach, delivering chemical ink deposition using technical pens filled with reagents and inserted into a desktop electronic plotter, is shown herein to be a versatile, low-cost, simple, rapid, reproducible, and high-throughput solution. The volume of the deposited ink was quantified gravimetrically, confirming that nanoliter volumes of reagents can be deposited reproducibly (e.g. 7.55 ± 0.37 nL/mm for a plotting speed of 10 cm/s) in detection zones of μPADs, typically spatially defined using wax printing. This approach was further investigated with regard to deposition of reagents in different geometrical forms (circular and linear), so demonstrating its applicability for preparation of μPADs with flexible design and application. By adjusting the plotting speed for linear deposition, lines with a relatively large range of widths (≈628–1192 μm) were created. Circular deposition was also demonstrated via delivery of reagents within wax printed circular fluidic barriers of a range of diameters (inner diameter = 1.5–7 mm). These capabilities were practically demonstrated via the fabrication of μPADs, based upon differing detection principles for determination of aluminum in natural waters using Morin as the fluorescent reagent. Traditional μPADs based on digital image colorimetry (DIC) were produced using circular deposition, whilst distance-based μPADs exploited linear deposition. Both types of μPADs developed using this method showed excellent precision for determination of trace concentrations of aluminium (average RSDs = 3.38% and 6.45%, and LODs = 0.5 ng (0.25 ppm) and 2 ng (0.5 ppm), for traditional and distance-based detection, respectively).