Characterization of enzymatic reactions occurring in untreated biological samples is of increasing interest. Herein, the chemical conversion of alliin to allicin, catalyzed by allinase, in raw garlic cloves has been followed in vivo by internal extractive electrospray ionization mass spectrometry (iEESI-MS). Both precursors and products of the enzymatic reaction were instantaneously extracted by infused solution running throughout the tissue and directly electrospray ionized on the edge of the bulk sample for online MS analysis. Compared to the room-temperature (+25 °C) scenario, the alliin conversion in garlic cloves decreased by (7.2 ± 1.4) times upon heating to +80 °C and by (5.9 ± 0.8) times upon cooling to -16 °C. Exposure of garlic to gentle ultrasound irradiation for 3 h accelerated the reaction by (1.2 ± 0.1) times. A 10 s microwave irradiation promoted alliin conversion by (1.6 ± 0.4) times, but longer exposure to microwave irradiation (90 s) slowed the reaction by (28.5 ± 7.5) times compared to the reference analysis. This method has been further employed to monitor the germination process of garlic. These data revealed that over a 2 day garlic sprouting, the allicin/alliin ratio increased by (2.2 ± 0.5) times, and the averaged degree of polymerization for the detected oligosaccharides/polysaccharides decreased from 11.6 to 9.4. Overall, these findings suggest the potential use of iEESI-MS for in vivo studies of enzymatic reactions in native biological matrices.