Microbial population and bioactive amine profile and levels of two lupin species (Lupinus luteus L. cv. 4492 and Lupinus angustifolius L. var. zapaton) and fenugreek (Trigonella foenum-graecum L.) seeds as affected by germination were investigated. Microbial population increased considerably mainly in the first stage of germination (2 days), then small changes in bacterial numbers were observed up to 5 days to levels between 7.8 and 8.9 log colony-forming units/g. Microorganisms belonging to the Enterobacteriaceae family were dominant for the legumes tested. Ungerminated legume seeds contained putrescine, cadaverine, histamine, tyramine, spermidine, and spermine. Bioactive amine levels found in fenugreek seeds were between 3- and 4-fold higher than those found in lupin seeds. The highest total amine levels were found in fenugreek seeds [162 mg/kg of dry weight (dw)], followed by L. angustifolius var. zapaton seeds (84 mg/kg of dw) and, finally, L. luteus cv. 4492 (46 mg/kg of dw) seeds. The concentration of individual amines showed a gradual rising trend during the germination period in all tested sprouts, reaching levels >3 times higher than those found in ungerminated seeds. After 5 days of germination, the fenugreek sprouts contained the highest amount of total bioactive amines. Tyramine was the predominant amine in both lupin varieties, whereas cadaverine was the main bioactive amine detected in fenugreek. The results of this work thus indicated that microbial population and biogenic amine levels in the studied lupin and fenugreek sprouts are not a risk for healthy consumers or for individuals with restricted activity of detoxification enzymes.