This paper describes a silica nanoparticle-modified microfluidic paper-based analytical device (µPAD) with improved color intensity and uniformity for three different enzymatic reactions with clinical relevance (lactate, glucose, and glutamate). The µPADs were produced on Whatman grade 1 filter paper and using a CO2 laser engraver. Silica nanoparticles modified with 3-aminopropyltriethoxysilane (APTES) were then added to the paper devices to facilitate the adsorption of selected enzymes and prevent the washing away effect that creates color gradients in the colorimetric measurements. Here we show three different enzymatic assays for compounds. According to the results herein described, the addition of silica nanoparticles yielded to significant improvements in color intensity and uniformity. The resulting µPADs allowed for the detection of the three analytes in clinically-relevant concentration ranges with limits of detection (LOD) of 0.63 mM, 0.50 mM, and 0.25 mM for lactate, glucose, and glutamate , respectively. An example of an analytical application has been demonstrated for the semi-quantitative detection of all three analytes in artificial urine. The results demonstrate the potential of silica nanoparticles to avoid the washing away effect and improve the color uniformity and intensity in colorimetric bioassays performed on µPADs.