The use of amino phases induced a significant increase of the bioluminescence for the high-performance thin-layer chromatography (HPTLC)-Aliivibrio fischeri bioassay. By this, the detectability of alkaloids was improved. Detection limits at the low ng per zone level were obtained for the five alkaloids berberine, palmatine, ephedrine, norephedrine, and methylephedrine. The influence of other parameters on this effect, such as fluorescence indicators and pH milieu, was proven to be insignificant. This implied that propyl amino groups linked to the silica gel layer might play a pronounced role in the improved visualization mechanism. The optimized bioassay was applied for profiling of alkaloid-rich herbal drugs such as Philodendron, Coptis, Tinospora, and Ephedra, leading to information-rich biofingerprints. The direct coupling of HPTLC to electrospray ionization mass spectrometry enabled unambiguous and straightforward confirmation of the bioactive ingredients.