Corydalis and Pseudofumaria are two closely related genera from the Papaveraceae subfamily Fumarioideae with Corydalis solida (C. solida) and Pseudofumaria lutea (P. lutea) as two representative species. Phytochemical analysis revealed significant differences in the quality and quantity of isoquinoline alkaloids, phenolic compounds and non-phenolic carboxylic acids between aerial and underground parts of both species. Using the Liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) technique, 21 compounds were identified: five protoberberine derivatives, three protopine derivatives, four phenanthridine derivatives, as well as three carboxylic acids, two hydroxycinnamic acids, one chlorogenic acid, one phenolic aldehyde, and two flavonoids. Moroever, significant differences in the content of individual compounds were observed between the two studied species. The phytochemical profile of C. solida showed a higher variety of compounds that were present in lower amounts, whereas P. lutea extracts contained fewer compounds but in larger quantities. Protopine was one of the most abundant constituents in C. solida (440–1125 µg/g d.w.) and in P. lutea (1036–1934 µg/g d.w.). Moreover, considerable amounts of coptisine (1526 µg/g) and quercetin (3247 µg/g) were detected in the aerial parts of P. lutea. Extracts from aerial and underground parts of both species were also examined for the antimicrobial potential against S. aureus, P. aeruginosa and C. albicans. P. lutea herb extract was the most effective (MIC at 0.39 mg/L) against all three pathogens.